Love through Pain
by monkey-in-a-tree
Summary: An away mission goes disastrously wrong. Rated M for future chapters: torture/violence/rape and bad language...basically stay away if you like 'clean' kind of fics. Elizabeth Weir/John Sheppard!
1. Chapter 1

**Crappy title I know but titles are pretty much my weakness; suggestions can be given, i will consider, or is it ok?**

**Disclaimer: only the plot is mine**

**AN: First SGA fic :)... And of course it's SPARKY! :D It gets more angsty and horror-like as the story progresses, this chapter is more of an introduction type thing.**

**Spoilers: Brief mentioning of 'The Storm'/'The Eye' but nothing major**

**Timeline: Not long after the events of 'The Storm' and 'The Eye'**

'So what are the rules?'

Elizabeth sighed as she lifted her head off her desk to look at John. They had been sitting in her office for hours going over the numerous rules of a society they were about to trade with. Usually they would not go through so much trouble but this particular society had three ZPMs at their disposal and were willing to trade them.

Even so, that did not stop the three hour lecture from seeming less strenuous.

'The Ongari are a suspicious culture with extremely harsh punishments for breaking their rules' she began reciting like she had been so many times that night.

'If you are believed to be a spy then torture and a painful death are guaranteed. When talking to an Ongarian one must keep eye contact or they will view it as an act of deceit and will resultantly arrest you. Only five offworld visitors are allowed at any one time, searches will also be conducted upon arriving at the gate and weapons will be confiscated inside the conference hall. Have I missed anything out?' she raised an eyebrow at the question.

She knew she had missed out one rule, probably the most important one to John, but it was the one rule she was getting tired of following.

John raised his eyebrow back at her, knowing full well she knew what she missed.

'Yes you missed out something which is fine so long as you know it and stick to it because if you don't I-'

'I know I know, John. But you need to realise I can look after myself. I don't need you, Teyla or Ronon with me all the time. I go offworld knowing the risks and accepting them. You should too; you can't protect everyone John'

John sighed thinking this talk was about to be getting a heck of a lot longer but he refused to back down. His feelings for Elizabeth and concern for her well-being would never let him back away from an important matter such as her protection. After the incident with Kolya and the storm, John felt an even stronger need to protect her, his best friend. Well, that's what he says she is anyway, which is the truth technically. But as of late his feelings for her have become much deeper than he wants to think.

'Look, 'Lizabeth. I know how you feel with this and I know you hate it but this planet is rough. The Ongari are very suspicious people, even the slightest mistake could result in severe consequences.' Elizabeth raised an eyebrow at this for it was only a few days ago that John was on trial by the Ongarian Government.

John seeing her expression realised what she was thinking about. He had to admit, that day was a shocker. There he was asking McKay where the hell they had just crash landed and suddenly this woman passes by wearing practically nothing! What was he supposed to do? But apparently checking people out is seen to be quite suspicious and therefore a criminal act on Ongaria. Thankfully Teyla had managed to get him out of the situation before any harm could be done.

'Forgive me John but I won't be making the same mistakes as you did. Not only do we know the rules now but we have gained some understanding from them. After all, they are willing to negotiate with us. Besides, I, unlike _some_, do not have a tendency to chat up passing people as soon as I arrive on a planet' she added giving John an amused look that made him fidget in his chair.

'Yeah yeah can we please stop bringing that up?' he'd had enough teasing about that from McKay and Ronon already.

Elizabeth smiled slightly at his discomfort. She would never openly admit it but hearing of John's predicament had scared her. Although when she heard of the nature of the imprisonment, a twinge of jealousy couldn't help but accompany that fear.

In the end it didn't matter; she was just glad he and his team were back.

'You haven't managed to distract me by the way. You **will **be accompanied by either myself, Ronon or Teyla at **all** times whilst on that planet.'

_Bugger_ thought Elizabeth. _Distraction plan failed_.

Sighing she got up and moved to sit on the desk in front of John.

'Look, I can-'

'I know you can handle yourself, just please... it's a precaution.'

She stared at him, John realising she was assessing some other way of talking him around the matter so he decided a change of tactic.

'Please 'Lizabeth, do it for me?' that phrase alone could not have swayed her fully which is why he added his best puppy dog look with it. He knew she couldn't resist them.

Sighing with frustration, for she knew full well what he was trying to do, she gave in, well... not completely.

'Fine! But I'm not taking a weapon with me' and with that she strode out of the room with a pat on John's shoulder bidding him goodnight.

_Damn. _She always did that. She refused to handle any weapon. He did at least manage to get her to agree to being trained in using basic weaponry and close combat but what use was it if she refused to hold one outside the training room?

Stubborn, just plain stubborn. But that's one of the things he loved about her.

_LIKED! Not going there John we are NOT going down that road!_

Shaking his head, a slight smile appearing on his face, he got up and made his way to his quarters nodding to the occasional person on the way.

Well, tomorrow will be interesting. And at least she agreed to have someone with her. That thought at least provided some sort of reassurance, although he couldn't help but feel particularly nervous about what the next day would bring.

Entering his quarters he decided to head straight for bed. By the time he was in bed his head was whirring with thoughts of what could go wrong and how he could avoid it.

He always grew anxious when Elizabeth went offworld but for some reason he felt a strong sense of dread about this mission.

The Ongarian Chief had requested to negotiate only with Doctor Weir and for some reason that made John feel very uneasy. Maybe he imagined it, but when the Chief stated his terms John couldn't help but feel that something was being hidden.

_Paranoid John you're just paranoid._

Turning on his side he closed his eyes and tried to will himself to sleep. He knew he should be as awake and alert as ever tomorrow. But that didn't stop him from thinking and dreaming of terrible things that could happen the next day.

If only he knew his dreams were much more than mere dreams.

**So, do I continue? Not continue?...Help me out here!**


	2. Chapter 2

**Disclaimer: only the plot is mine**

**AN: Next Chapter will be the last one that is below the M rating. Then things get good :)**

**Warnings: mild abuse**

**'_John...help me. Please John, stop them. John!'_**

**_He stood there watching her, watching as she was lifted and dragged away from him. Her clothes were torn and dirty. Her hair in complete disarray. But worst of all was her face. The usually green eyes that were so full of life and strength were now a dull grey, tainted with pain and defeat. Her usual pale complexion had somehow paled further so that she appeared to glow against the dark walls of the cave._**

**_He continued to stand there and watch as she was slammed against the wall. He tried to run to her but he couldn't move. To his surprise he could shout but it did nothing; it was as if she couldn't hear him. As if he wasn't there with her._**

**_He stared in horror as they began beating her again. First to the stomach, then to the head. John shouted with all his breath whilst fighting against the non-existent restraints, continuously prompted by the blood-curdling screams emanating from her._**

**'_Elizabeth! Leave her alone! ELIZABETH!'_**

**_He tried with all his strength but still couldn't budge an inch. He gave up, repeatedly telling himself it wasn't real, hoping against hope that it wasn't real._**

**It can't be happening, this cannot be happening! I would never allow it, I could never stand back like this!**

**_With that thought John moved. Not wasting a second he started running after Elizabeth who was now being speedily dragged out of the room. He ran as fast as he could but as soon as he turned the corner she was gone. He turned around but found himself in a different room. No, not a room...he was outside somewhere. Studying his surroundings John suddenly felt a growing sense of unease._**

**Why is this so familiar? I've never been here before in my life but somehow I know this place...and I don't like it.**

**_He continued his study, all the while trying to place the unsettling feeling._**

**_The trees were tall and very green, abnormally so. Beneath them sat colourful bird-like creatures with wings the size that would be associated with a dragon. Behind him were some creatures very similar to that of the Earth Lion, only they had three legs (_****How that's supposed to work I'll never know _thought John)._**

**'_John Sheppard, it is time'_**

**_Spinning around John saw an old man who closely resembled the Ongarian Chief._**

**'_Where is Elizabeth!' John demanded immediately._**

**'_She is undergoing her punishment' replied the Chief._**

**'_Punishment for what?' asked John, slowly edging closer to the Chief so that he was in a position to attack if necessary._**

**'_You will see' and with that he was gone, leaving John alone but back in the cave._**

**'_WHAT IS SHE BEING PUNISHED FOR?' _**

**_John continued his screaming towards the roof, trying to get some sort of reply. He was suddenly cut short by a very quiet yet noticeable voice._**

**'_John...help me'_**

**'_Lizabeth! Where are you?'_**

**_He couldn't see a damn thing and was too afraid to move in case he bumped into her._**

**'_Help me John, please. Don't leave me John'_**

**'_I won't! But I need to know where you are...please?'_**

**_His voice became so pleading it was barely recognisable to himself. The desperation to find her was overwhelming him. _**

**_Suddenly, the cave was filled with a dim light. Looking towards the door he saw Elizabeth, huddled in a corner with her head bowed low. _**

**'_Lizabeth!'_**

**_He made to run towards her but suddenly his vision started to cloud. He could hear a voice, a man's voice, calling to him...telling him to wake up?_**

**What the hell is going on? Go away, I need to get to Elizabeth I can't leave her!**

**_He continued to struggle, trying to fight the fogginess overcoming his vision. He tried to hold onto Elizabeth's cries of 'John don't leave me!' but the man's voice was persistent. John was being pulled further and further away from Elizabeth and closer towards the waking world._**

'Sheppard!'

John awoke with a start, heart beating rapidly against his chest. He looked around his room, thankfully taking in the familiar sights.

_It was just a dream. Thank fuck it was just a dream._

John barely had time to acknowledge the massive wave of relief that overcame him before...

'SHEPPARD! which was soon accompanied by a series of poundings against the door.

'McKay? What do you want?'

'GET UP NOW! YOU BETTER HAVE A GOOD REASON FOR BEING LATE OR ELIZABETH WILL KILL YOU!'

John glanced over at his clock which read 08:00 hours.

_Crap! I was supposed to BE there half an hour ago!_

'SHEPPARD!'

'YES MCKAY I HEARD YOU! Now shut up and let me get ready!'

John sighed as he heard McKay leave whilst muttering something under his breath.

_Crap, Elizabeth really is going to kill me!_

Getting out of bed he groggily made his way to the bathroom.

_What can I tell her? 'I overslept because of a horrible nightmare that involved you getting brutally beaten and some strange 3-legged creatures?'_

Not only did that sound creepy but it was nowhere near a good reason. Fact of the matter was he overslept, plain and simple.

_I'd rather face those damn bugs than get put down by her although...damn, I hate those bugs._

Groaning at the thought of the lecture awaiting him, John continued getting ready. But not once did the thought of his dream being so much more than a dream, leave him.

**Still good? Review because it'll make me happy! (and keep writing :P)**


	3. Chapter 3

**Disclaimer: only the plot is mine**

**AN: Had to edit some things; I'm one of those where small things can really bug me. Its nothing massive; few typos and grammar issues so you wont need to re-read it. I've started chapter 4 so expect an update soon!**

**Also, re-capping chapter 2 if you haven't read it is a good idea**

'Ah, there he is! Sleeping Beauty has finally arrived!'

'Shut it McKay!'

John was not in the mood for any wind-ups from anyone at the moment, especially McKay. The feeling of dread had grown more intense with every step he took towards the gateroom. Not only that, but he was starting to feel physically sick from it. Plus he still had to face Elizabeth and he was sure that would not end well.

'Major Sheppard, nice of you to finally join us.'

_And so it begins..._

John turned to face her deciding to go with the truth, although minus the dream.

'Sorry, I overslept. Must have slept through my alarm or something' he mumbled sheepishly whilst moving a hand through his already messed up hair.

To John's surprise she didn't snap. Instead she tilted her head in that way she did when she was thinking about something. And was that...no. A look of concern across her face?

_I must be more tired than I thought._

Shaking his head he moved to address his team.

'OK, so we all know the rules, what to do and what not to do. Ronon and Teyla, I want to make sure that one of us is accompanying Doctor Weir at ALL times. Clear?'

'Hey! Why can't I look after Elizabeth?'

Eyebrows were raised towards McKay by everyone present, a few random comments even being made by various personnel as well.

'Right...' was his mumbled response.

Elizabeth who was torn between amusement and not liking the idea of being 'babysat', called up for the gate to be dialled.

She glanced over to John who had been unusually quiet. He could have easily slipped in a few retorts to Rodney just now but he didn't. This and the fact he was late when she was due to go offworld worried her significantly. She knew how anxious he could get and how protective he was, especially over her. It was for this reason why it was so discomforting.

_What are you thinking about Major?_

Her thoughts were broken when John turned to look at her, obviously sensing her gaze. He tended to do that a lot. He smiled and she smiled back, but from the look on his face it wasn't as genuine as she thought. Instead she moved closer to him, making sure only he could hear her.

'John, are you alright? If you don't feel well then—'

'I'm fine and I'm going. You're not setting foot on that planet without me there with you'

The authority and determination that could be heard in his voice shocked her. They both cared about each other, probably more than was appropriate, but he had never forced the issue as strongly as he did just then.

She gazed into his eyes and said nothing, just studying him.

_He's sad. _She noted._Something is bothering him; only once I've seen him look at me like that. After Kolya..._

She opened her mouth to speak but before she could, he turned to face the rest of the team.

'OK team, lets go'

It had been three hours since they had arrived in Ongaria. Only one other person was allowed in the conference hall with Elizabeth and naturally, that was John.

They had been trying to negotiate an exchange for the ZPMs. So far, the only thing the Ongarian Chief would trade was one ZPM for two jumpers. Elizabeth naturally disagreed to this but at the same time, had to do so tactfully so as not to offend the chief. She had tried explaining to them that only those with the ATA Gene could pilot the jumpers but the Ongarians being who they were, thought it was just a ruse. She really couldn't win with them.

John meanwhile had been thinking back to his dream, trying to decipher the meaning of it.

'Major?'

John snapped his head towards Elizabeth, cursing himself for zoning out again.

'Yes Doctor Weir?' he replied, wincing at the hoarseness of his voice from its lack of use that morning.

'Is your colleague unwell?' questioned the Chief.

'Sorry' he cleared his throat. 'I urm... I just didn't get a good nights sleep that's all. Please continue' John turned to face the Chief fully, partly to keep eye-contact easier and partly to escape Elizabeth's studying gaze that was making him even more uncomfortable.

'I was saying,' began Elizabeth, eventually pulling her eyes away from John.

'that Colonel Sheppard could pilot one of our jumpers to show you how the ATA Gene effects its ability to function.'

'But why can't you show us Doctor Weir?'

John's attention snapped fully to the Chief. The dread that had somewhat calmed now flared into full life again. He had no idea why but that question was not right. The way the Chief had asked was suspicious to John, holding some sort of a double meaning.

He gasped for air, his head spinning so fast that seeing was becoming impossible. He could feel Elizabeth's concerned gaze boring into his back and could almost hear her brain whirring with thoughts as to what was wrong with him.

But still he pushed all his feelings away, trying desperately to focus on the Chief and why that question had caused such a response from him. Somehow John knew this was where things would change but he had no idea how he knew that let alone why he knew that.

'I do not possess the ATA Gene unlike Major Sheppard here' came Elizabeth's eventual reply.

_No, this isn't right. She shouldn't have answered that. I don't know why but she shouldn't._

'And why is that Doctor Weir?' continued the Chief.

John burst out of his chair knowing that things had to stop now. Elizabeth stared at him, confusion and concern written all over her face. She opened her mouth to question him but soon closed it, realising something was more than wrong with him.

'I'm sorry but would it be possible if we took a short break?' she asked the Chief instead.

'Of course. But please, stay in your rooms. We do not take kindly to people wandering around.'

Elizabeth gave a polite nod towards the Chief but was focused solely on supporting the now shaking John. Slowly she led him out of the hall towards his room.

**_Screaming, who was screaming?_**

**'_John!'_**

**_Who was that?_**

**Wait, I know her voice, I would know it anywhere.**

**'_John! Please come back to me John I'm here. Focus on my voice John'_**

**Where was here? And for that matter where the hell was he?**

**'_The time has come John. She will be punished'_**

**_John froze at the sound of the Chief's voice, a sense of déjà vu accompanying his worry._**

**'_Why is she being punished?'...'ANSWER ME!'_**

'John Sheppard wake up NOW!'

John snapped his eyes open and came face to face with none other than Elizabeth.

'John, thank god you're awake, you had us worried there' she gently smiled down at him, her hand holding his he realised.

'Wha..us?'

John looked around to find his team all around him, all of them with worried yet relieved faces.

He tried to get up only to be firmly pushed back down by Elizabeth.

'Not so fast flyboy, you need to stay put.'

He was about to protest but she fixed him with one of her stares.

'What the hell happened? And where am I? Last thing I remember we were leaving negotiations.'

Elizabeth smiled as he finally gave in and resettled on the bed.

'You're in my and Teyla's room. I brought you here after we left the negotiations. You started to shake and kept telling me...things.' he noticed her pause at this.

'I realised you wouldn't make it to your room so I brought you to ours. Thankfully Teyla was here so she could get the others. You've been out for about ten minutes.' She added, realising what his next question was going to be.

'Yeah, ten minutes of pure kicking and screaming. What the hell were you dreaming?'

John looked over to Ronon, trying to decide what his answer was going to be when suddenly, thankfully, he was saved by a knock on the door.

'Enter' called Teyla.

A timid looking Ongarian entered. _The Chief's servant_ John noted.

'Sorry to interrupt kind guests but the Chief wishes me to deliver a message to you. He wishes Major Sheppard a speedy recovery and is willing to postpone the negotiations until tomorrow afternoon. In the meantime, he has invited you Doctor Weir, on a tour around the gardens. One guard may also join you.'

Elizabeth glanced at John well aware of the argument that was about to take place.

'Thank you for your time. And please send my thanks to the Chief. I would appreciate negotiations being postponed. As for the tour, I'd be honoured' she smiled at the Servant as he moved towards the door.

'I will notify the Chief. Remain here please and you will be escorted.' With that he nodded and left the room.

'Elizabe—'

'John, listen to me. You are ill. You're going back to Atlantis with—'

'Lizabeth I'm—'

'I said John, you are going back to Atlantis. That's NOT a request. You are sick and you need to see Carson. Ronon I want you to take Major Sheppard to the gate and back to Atlantis. And I'm ordering you to make sure he stays in the infirmary until Beckett says otherwise is that clear?

A nod and the sound of Ronon's gun being set off kill and to stun was his only reply.

John couldn't stop staring at Elizabeth. She never acted like this.

'Lizabeth, can we talk? Alone.'

Everyone else immediately cleared the room.

'John I—'

'Please Liz, just listen to me a minute'

She stopped and glared at him. He knew damn well how she hated having her name shortened like that.

'Thank you' he said, smirking slightly as she glared at him.

'Look, I dunno what I said to you but obviously you seem pretty pissed off about—'

'Pissed? You think I'm pissed off? Is that what you think? John I am everything BUT pissed right now. Well maybe not NOW now but before it was—'

_OK, what the fuck did I say to her? _John just stared at her as she continued to rant. Never before had he seen her this worked up about something and he had to admit, albeit being scary she did look quite attractive when riled.

_Bollocks, she stopped. And she's staring at me. Bugger what did she say. Oh you are gonna pay John you are gonna wish you were never born!_

She sat back down on the bed and grabbed his shoulders, almost shaking him, a terrified look in her wide eyes.

'John! What the hell is wrong with you! I knew I shouldn't have let you come here I knew something was wrong this morning why did you tell me it was fine?' she moved away and began pacing around the bed.

'Argh no this is my fault it's all my fault I—'

John practically shot out of the bed, not caring about the dizzy feeling overpowering his head. He grabbed Elizabeth buy the shoulders and turned her to face him.

What he saw broke his heart. She was crying, trying and failing to hold back tears which he knew were for him.

He did something he had never done before and hugged her while gently rubbing smooth circles on her back.

'Shhh, it's ok. I'm ok and it's not your fault. I just haven't been sleeping much. Whatever I said to you I'm sorry for. I probably had no idea what I was saying so I am so sorry if I offended—'

'No! No John you didn't offend me. I'm just...confused. It was so sudden and to see you screaming like that...'

She trailed off, obviously debating whether to pry further. Eventually she hugged him tighter, deciding she had to know.

'John, what were you dreaming? What was causing you so much pain?'

He buried his face in her hair, noting her familiar scent and taking comfort in it.

_Maybe I should tell her? I hate worrying her and I can't lie to her..._

Elizabeth could practically hear his internal argument of 'do I tell or not' and was about to tell him to forget it when he finally decided to open up.

'I dreamt... I dreamt something horrible. Something I don't want to ever happen. I...urm...I uh...Its a kind of...you urm...'

_Wow Sheppard, that's some smooth talkin there. I'm sure she completely gets your point! Idiot..._

'John' Elizabeth smiled slightly at his hesitant manner. That's one of the things she loved about him.

_Except for the hair _she thought. _Oh and that cute little pout of his._

She pulled away smirking at that last thought.

'Never mind John. It was just a dream. I'm here with you. Nothing is going to happen'

With that she smiled and took hold of his hand, her smile widening when he gripped it back.

'Urm, sorry to interrupt kind guests but the Chief is ready for your tour now. Is Major Sheppard accompanying you Doctor Weir?' asked a slightly embarrassed servant.

'Yes I am' cut in John before she could say anything. He turned but only to be met by a completely un-amused glare from Elizabeth.

'Please Lizabeth. I can't leave you alone and right now I don't want you to leave me. It's a stroll around outside. God knows we could both use some fresh air. I promise you after the tour we can discuss me going back to Atlantis. Deal?' and just for added measure he added his best smile.

_Damn him, he knows I can't say no to him and that smile! We need to have words later..._

'Fine, but you have to promise to tell me if something is wrong. Even if you're feeling dizzy or I'll never forgive myself. Deal?' she added sweetly afterwards.

_Two can play at that game Major! I know you hate anyone but you taking the blame._

Her smile faltered slightly as she saw that serious look in his eyes as he studied her. After what seemed like ages he finally replied.

'Deal.' And with that he pulled her towards the door to follow the servant, never letting go of her hand.

'And now we come to our best green area. 'The Forest of Tranquil', a truly marvellous place if I may say so myself.'

Elizabeth followed the Chief, nodding occasionally to his words. They had been strolling for hours with the sky gradually growing dark. She could feel John slowly weakening next to her but every time she turned to question him he squeezed her hand slightly to tell her not to worry. It had surprised her when he kept hold of her hand. In fact he refused to let go of it for the whole tour. However, as the chief mentioned the forest of tranquil she couldn't help but realise his grip tightening slightly.

'John, you ok?' she whispered as they followed the Chief.

He nodded slightly, although his face and body expressions said otherwise; his shoulders were tense and his lips were pressed tightly together. His eyes were frantic, as if searching for something but as they continued walking she realised he kept returning his gaze to the Chief who was now a good few metres ahead of them.

'John, what's up? Please, tell me.'

'Nothing'

'You promised' she pleaded, knowing full well this would get to him.

'Lizabeth' he stopped. 'I don't like this place. Please, we need to go...Now.'

'Look John, we're almost done. The Ongarians rarely take guests on tours and this is the last sight we're seeing. This could do wonders to our relations. I know you're feeling uneasy but do it for Atlantis. You know we need those ZPMs, especially with the Wraith at our doorstep/'

John stopped, pulling Elizabeth with him.

'Atlantis is not worth what I could lose if we go further. Please Elizabeth.'

'John?'

She gazed into his eyes, knowing but not believing what he was implying. She placed her hand against his cheek, loving how he leaned in towards her touched. She smiled slightly as he leaned forward. When only a small space remained between them he paused, giving her a chance to pull back.

She didn't.

She leant forward, closing the space so both their lips met. His tongue ran across her lower lip begging for entrance. She gladly granted it.

They continued to kiss, the passion increasing with every second. He was gentle, his hands holding her to him and softly drawing random shapes on her hips with his thumb. Her hands were in his hair, keeping him locked to her until they finally broke for some much needed air.

He leant his forehead against hers.

'John?' she whispered.

'Yeah Lizabehth?'

He waited, dreading that she was about to tell him that the kiss was wrong.

'John. I don't regret that. In fact, I would like it if it could happen again.'

She smiled up at him and gave him a quick kiss on the lips before moving away to study their surroundings.

'Damn' she exclaimed after a while.

John looked questioningly at her, trying to focus on what she was saying rather than how the setting sunlight was playing with her features.

'John?'

'Mmmm?'

'John!' she playfully slapped his arm realising he hadn't been listening to a word she'd been saying.

'I said' she repeated, 'we lost the Chief. We should make our way back. I think it's pretty straight for—'

She didn't finish her sentence. John gazed in horror as Elizabeth's skin grew frighteningly pale, her lips turned blue and her eyes grew dark circles around them. She swayed and fell, John catching her before she hit the ground.

'Elizabeth!'

He lay her down and leant over her, praying he'd find a pulse. He noticed a tiny dart sticking out of her neck.

_Shit, someone's here._

He instinctively snapped his head up and reached for his pistol, only to realise he'd left it too late.

A dart stuck the side of his neck and his vision immediately blurred. The uneasy feeling that had been living within John rose to its full potential and wreaked further havoc on John's systems. He fell beside Elizabeth gasping for air. His chest was tightening and every breath was harder to take than the next. He stared up at the sky through the tree they were lying under. His vision started clearing again.

_Wow, that's one fucking tall tree. And it's very gr-_

'Fuck.'

John stared. He stared up at the tall tree. The very green tall tree. Maybe something he'd describe as abnormally green and tall.

He glanced around hoping beyond hope he was wrong.

_Please it can't be. Surely I would have noticed!_

But sure enough he was wrong for beneath a nearby tree slept a colourful bird-like creature with wings the size that would be associated with a dragon. Further down John's line of vision sat a pack of creatures very similar to the Earth Lion, only they had three legs..._how is that supposed to work?_

'No, No, No, No' John couldn't stop repeating it. His vision blurred again and his eyes were becoming too heavy to hold open.

'No' he mumbled

'Liz'beth. Must, need...you need to go...have to save you...have to...cant'

John heard the sound of approaching footsteps that soon stopped right by him and Elizabeth. He heard a lot of shuffling around Elizabeth and soon realised they were moving her onto a stretcher because they soon did the same to him.

John willed his eyes to open a fraction but he could only see shadows. Someone was standing above him, looking down at him. And then came the voice..._his_ voice; 'It is time John Sheppard. She will be punished'

And then the darkness claimed him.

**Would like some feedback on the last part; did you get how it linked with chapter 2 or was that really unclear? Not quite sure with that bit so feedback much appreciated!**


	4. Chapter 4

**OK at the beginning of the story I said it was set shortly after 'The Storm' and 'The Eye' but we'll make it after 'Runner' because I've already included Ronon in this so yeah… IM ONLY HUMAN, MISTAKES ARE ALLOWED!**

**AN: Sorry for the wait, life has been really busy lately. But I did eventually finish the chapter so enjoy!**

**Spoilers: None…well, Ronon but does he count as a spoiler? Let's include him as one coz I love him!**

**Warnings: Language from now on will probably be quite strong. Also the M-rated stuff starts from here on.**

'Get up _Doctor_!'

The mocking snarl was followed by a harsh kick to her ribs.

Elizabeth groaned as the pain coursed through her body. Barely raising her head, she looked around to find herself on the floor of a small grey room.

'Nice of you to finally join us' came the voice again.

Elizabeth looked round to see a man standing not too far from her.

_Shit _she thought; the man who appeared to be guarding her was not only a few feet taller than she was, but he was also a good two times wider than she was…and it wasn't fat.

Elizabeth slowly stood up to face the guard, biting her lip when the pain down her side intensified.

'Who are you and what do you want…and what have you done with Major Sheppard?' she added realising his absence.

The guard smirked as he sauntered over to her, his hands curled into great big fists. Elizabeth backed away as he approached but he was too quick; his hand had darted out to seize hold of her throat.

'Listen Weir, I ask the questions around her, NOT you. Now, you have five minutes before I come back in here so you better be ready to go by then and I don't want to hear ANY more questions. Clear?'

Elizabeth gasped as his grip tightened around her neck. She tried to claw at his hand to loosen it but all that did was make him hold her tighter. She didn't see much of a choice except to play along for now so she nodded slightly and was relieved when he let go.

'Five minutes' he reminded her then walked out a nearby door.

Elizabeth rubbed her neck as she sank to the floor. She sighed and began looking around for any possible escape routes, something she shortly realised was a futile effort; the walls were made of a thick stone with absolutely no cracks, or even dirt, on them and there was only one heavy-looking metal door, which more than likely had the massive guard on the other side of it. The ceiling was like the walls; thick and only marked with a single light hanging from it. Not to mention the fact that it was ridiculously higher than your average ceiling.

_Bugger. How the hell do I get out of here? Wherever the hell here is. What happened?_

She tried to recall how she got there but couldn't.

_OK, the last thing I remember…I was in 'The Forest of Tranquil', being led by the Chief, with John…we got lost and…oh yeah, I remember._

She smirked as the memory of their kiss came back to her. Her smile however, quickly vanished when she realised once again that John wasn't with her.

_Where have they taken him?_

She got up and began to pace, thinking of possible answers.

_John, he said we should have left…he must have known. But that's not possible! I'm sure this is all a misunderstanding._

Her thoughts were rudely interrupted when a hand seized her shoulder.

_Shit, when did he get back in here!_

'Your five minutes are up, now out!'

He pulled on her shoulder and dragged her towards the door.

Almost as soon as she stood outside she found her vision blocked as a bag was thrown over her head. Two more men seized her arms and continued to drag her further, the massive guard still behind and now holding the back of her neck.

'Try anything and we don't hesitate to kill you' came a whisper against her neck.

Elizabeth jumped slightly at the unexpected voice but decided just going along with things would be the best course of action at that moment.

_Not too long now_ she thought._ Atlantis will be coming for you. They won't leave you behind…John won't leave you behind._

'Doctor Elizabeth Weir, current leader of the Ancient City Atlantis. Your trial has now commenced. Step forward'

Elizabeth was dragged forward and sat roughly down on a hard metal chair. A vast amount of noise was made as the surrounding guards chained her to the chair.

When they were finally done the bag was removed from her head.

Elizabeth gasped as she stared at the hundreds of people seated all around the room. Her eyes however were quickly drawn to the people sitting straight ahead of her; the Chief and the rest of the Ongarian Council sat in a long line of high and fancy looking chairs.

_OK they're in on this, maybe not a misunderstanding then._

'Doctor Weir, you have been found guilty of many crimes against this galaxy, the most prominent of which are your deceitful reign of the ancestral city and your awakening of the Wraith. This trial is not debating your verdict but your form of punishment. The council has already found you guilty as of yesterday afternoon when you freely acknowledged that you are not of ancestral heritage.'

Elizabeth froze as she remembered the meeting that took place in which she did indeed freely condemn herself. Her eyes widened as she remembered John's behaviour.

_So John did know. Bugger, I should have listened to him. Why didn't I listen!_

'The Ongarian public have supplied some suggestions on your punishment. Usually a death sentence would be in order however, the Ongarian Council believe that death would not suffice and that a less...kind punishment should be given. We are therefore left with two options.'

Elizabeth watched, stunned as the Chief shuffled through some data on his pad. Her heart was pounding against her chest and she knew her diplomatic face was slowly failing her as she struggled with the shock and disbelief of the situation.

She tried to calm her racing heart but failed miserably as she saw the Chief lean over to look at her, an evil smirk playing across his face.

'As I was saying, your two options include long-term captivity in our holding cells or we will offer you up to the Wraith as a gift for their generosity. The latter would be the most beneficial to us however, the rest of the council are not happy with giving you such an easy getaway. You are a resourceful and smart woman Doctor Weir, we don't deny that. If we leave you to the Wraith there is a chance your people could rescue you, or even you could escape yourself.'

Elizabeth stared at them in disbelief.

_They're Wraith worshippers! How the hell is this happening!_

'Chief I don't know what you-'

She was cut off with a sharp slap across her face. She turned to glare at the enormous guard who had, at some point, come to stand behind her.

'Silence! You have no say in your verdict, you are guilty and therefore stripped of your rights!'

Elizabeth was about to speak but thought better of it when the nearby guard grunted.

'That's better' remarked the Chief.

'Now, the debate is open to the floor. The Wraith would appreciate the leader of Atlantis being delivered to them however, they can be ignorant to her and the Atlantis inhabitant's abilities. Escape is very possible. Having said that, there is a better chance she will be fed upon and can therefore experience what she has unleashed upon this galaxy. This is something many of you who have lost loved ones to the Wraith wish for.' He paused as a murmuring of agreement spread the room.

'The alternative is sending her to the Atarus working grounds. There she can learn discipline and suffer for what she has done. We have talked with Councillor Rika and he has even agreed to a…_special_ form of treatment.'

At this the murmuring once again spread only this time louder.

_Oh crap, I hope Atlantis finds me soon. Negotiating my way out isn't looking too good right now. _

Elizabeth focused once again on her surroundings. The public and council were in a loud discussion about her punishment. She tried to look behind her but couldn't turn enough with the chains around her.

_And fighting my way out isn't an option either._

She started to panic as the helplessness of her situation was settling in. Gradually she willed herself to regain her composure and calm.

_Think Elizabeth, calm. You need to find out where you are first. Only then you can know how hopeless the situation is. Only then can you know what to do so calm. Calm, calm…he won't leave you. John will never leave you…I need to find him. What happened to him?_

Her heart started its irregular pounding once again as fear for John overwhelmed her head.

_Dammit Elizabeth! Hold onto that thought; John will come for you. He will save you...Crap what are they saying?_

'—Weir will be sentenced for life in the Atarus working grounds to pay for her crimes against this galaxy. No further trial will commence, ever. The punishment and verdict are permanent and binding under the Ongarian criminal laws. Doctor Weir, you will be transported in eight hours. Escort her back to her cell Gyra.'

Elizabeth was too overcome with shock to realise the large guard, apparently named Gyra, start to undo the chains.

_This cannot be happening…_

But it was. She tried to protest again but was quickly cut short with a punch to her stomach, shortly accompanied by a roar of approval from the Ongarian public.

Elizabeth preferred to leave uninjured so allowed herself to be dragged away. The bag was placed on her head once more as she left the room.

'Eight hours huh? I wonder what fun we can have in eight hours?' Elizabeth bit down on her lip as she felt Gyra's hand circle her hip slowly, torturously.

_Calm Elizabeth. We never leave our people behind. They will come for you. John will come for you, just stay strong. John will come for you…_

'Wait here' muttered Gyra to the other guards. With that he took Elizabeth's arm and shoved her back into the cell, making sure to lock the door after him.

Elizabeth was terrified. She stood there, trying to figure out where he was.

She could hear him panting lightly, somewhere off to her right. She stood from where she fell and continued to hold her head up high.

_Calm Elizabeth, stay strong. John will save you. He won't leave you._

She took in a shaky breath, a good idea of what was about to happen. Even so, she stood her ground as his footsteps were finally heard coming towards her.

'Well well, the great Doctor Weir is afraid.'

He was circling her now, reaching out to her at random intervals to catch her off guard. It worked, every time he touched her she flinched.

'You think your boyfriend can come and save you don't you? Well let me tell you this; he won't'

Elizabeth stumbled as he pulled her towards him.

'Where is he?' she demanded, glad that her voice didn't reflect how terrified she was.

He pulled her tighter towards him, his arm tightening around her neck with every breath.

'Don't you remember what I said about questions? Only _I_ ask them'

He threw her to the floor and pulled the bag from her head as she fell.

'Don't' she stammered as he moved slowly towards her.

'Don't what?' he sneered.

He grabbed her arm and lifted her with ease, making sure to slam her against the nearby wall with full force.

She tried to struggle against his grip but he pressed his body against her to completely halt her movements.

He stared at her, looking her up and down.

'Not bad' he commented when his eyes reached her chest level. 'Not bad at all'

He moved slightly away, which was all she needed. The movement had left her right leg without restraint; she kneed him and thankfully hit his 'special place'.

He crumpled and she used the opportunity to bolt for the door, internally cursing herself when she discovered it was locked.

_Fuck! Nice one Liz he fucking locked it and now you really pissed him off!_

She turned around to see him standing up.

_Damn this guy doesn't go down easily._

She watched him carefully as he slowly stumbled towards her, a pure look of anger reflecting clearly in his eyes. She got ready to run out of the way but he stopped about two metres in front of her and stared at the door behind her.

'Guys, I think you can get in on this!' he shouted to it.

Elizabeth was still processing his comment when the door opened and two guards entered the room and grabbed her arms, shutting the door as they slammed her against it.

Gyra moved towards her and grabbed her face in one of his big hands.

'I'll make you regret that you piece of FILTH!'

He punched her with his other hand in her stomach and laughed as she recoiled.

'Strip her' he called to the other guards once he'd finished throwing a few more hits at her.

They had obviously done this before because within a minute, Elizabeth was being held on her back, pinned to the floor by the two guards, lying there in just her underwear.

She'd been too preoccupied with fighting the guards to realise that Gyra had his trousers and pants down, that was until he stood above her, fully erect.

'Black see-through lace huh?' he remarked at her underwear.

He nodded his head towards the two guards, informing them to remove her bra and restrain her upper boy whilst he took hold of her legs and forced them apart.

'I'm beginning to like you' he leered down at her as he began to settle between her legs.

Her eyes widened in horror as he looked her over once more, his gaze lingering on her breasts before he grabbed one of them painfully in his far-from-gentle hands.

Reflexively she cried out, continuing to do so as he lowered his head to her other breast and bit her nipple, hard.

She whimpered as he lifted his head to meet hers, his hand still squeezing her breast painfully.

'Not so strong now are we Doctor? Still think your boyfriend will turn up to save you? Well he won't. You want to know why? Want to know where he is?' Gyra pressed his lips against Elizabeth's, forcing her lips to part and give way for his tongue. She resisted as much as she could but couldn't fight off all three guards holding her.

He continued to kiss her, his intruding tongue suffocating her. As he did his hands slithered down her body until they reached her panties.

She tried to scream as she felt him begin to slide them down but he forced his mouth harder against hers. Instead she bit his lip and the metallic taste in her mouth told her she pierced his skin. He growled and responded by forcing two fingers past her pants and into her body, his nails scraping against her insides.

She gasped and screamed, trying with all her power to fight against the guards and against the pain he was causing within her; his nails were sharp and he knew that. Every time he moved within her he made sure to dig into the surrounding flesh.

'That'll teach you to bite me!' he said once he finally released her bruised lips from the brutal kiss.

He withdrew his hand from within her after a few more thrusts and brought it up to show her; an abnormal amount of blood was covering a large portion of his hand. He smirked as he wiped it against her stomach.

'Where is John?' she weakly demanded, trying to hold on to one sane thought to keep her going. The mere thought that he could come to save her was enough to keep her from giving in to the pain.

Gyra paused at the sudden question from her and after a while smiled as he considered what answer to give her.

Leaning forward he whispered the one word she had hoped never to hear, the one word that in an instant destroyed all meaning to go on.

'Dead.'

And with that he entered her swiftly, brutally and without any warning.

Elizabeth screamed as she felt her inner muscles protest at the sudden intrusion. She was nowhere near ready for him and never would be. Not only that but as expected from someone of Gyra's bulk, he wasn't small at all.

'I see it's been a while for you' commented Gyra casually as he kneeled above her, relishing her pain.

'So tight, not that I'm complaining, it's more gain for me' he smirked.

'Major Sheppard and you didn't get this far did you?' he continued, pausing briefly as he suddenly realised a new way of torturing her.

He once more leaned down to her ear.

'You haven't come for him yet have you?'

Her only response was a whimper as she realised where he was heading.

'I wonder what he'd say if he knew you came for me' he sneered as she closed her eyes against the oncoming tears.

'But then again, no need to worry. He's dead. Gone forever and you'll never see him again'

'Bastard!' she shouted and then spat in his face, all sensible thought fleeing her mind.

She didn't care about the murderous look Gyra had plastered on his face. She didn't care how he had started to rapidly thrust in and out of her, painfully tearing at her tender flesh. She didn't care as he began to suck her breasts until they were raw. She didn't give a damn about the two guards hold her arms and chest down whilst laughing at her pain. She just didn't care. John was dead and that was the only thing that registered in her mind.

All she could think of when Gyra began to vigorously rub her clit was John.

When Gyra was whispering phrases like 'come for me' in her ear she ignored them, focused solely on fighting the sickening pleasure he was bringing to her, fighting it for John.

She had to admit, Gyra knew his way around. He was rough with her but he knew the perfect way to stimulate her clit.

She tried to fight the oncoming climax with everything she had left. She tried to tell herself not to give in, to stay strong for John.

But as she climaxed she realised that there was no John to stay strong for. He was gone, she was alone.

Gyra thrust once more until he released his tainted seed inside her, relishing the sound of her heartbroken screams.

Satisfied, he withdrew from her and kicked her stomach so she recoiled. He nodded to the other guards before he pulled his clothes on and left, signalling that they were free to have their fun with her.

Elizabeth lay on her side, pain dully throbbing in every part of her body. She was aware of a door shutting then locking, she was aware of the other two guards shifting their grip on her and then unzipping their pants. She was aware as each one took turns, thrusting in and out of her. Each moment, each feeling fading into nothingness.

She could have fought, but she didn't. Instead she lay there, trying to block out the pain and the disgusting pleasure that was being forced upon her, one word constantly going through her mind.

_John._

One thought torturing her more than Gyra or the other guards ever could.

He was gone.

_Dead_.

And she would never see him again.

_**Meanwhile…**_

'Sheppard, wake up!'

John blinked groggily as he stared up at the infirmary ceiling and then at the blurry vision of Rodney next to him.

'Ah, here he is! Sleeping Beauty!'

_Sleeping Beau- Hang on. De ja vu or what._

'It's about time. We were wondering if you were ever going to wake up!' continued Rodney as he poured a drink of water and handed it to John.

_Hang on, is Rodney? No! He just poured me a drink! Wow I must have been out for a while._

Nodding his thanks John took the glass and slowly drank whilst Rodney lifted his head.

_Hang on, he's holding my head up? Seriously, what the hell happened to make him act all weird and caring?_

'What happened to you down there?' questioned Rodney, completely oblivious to John's thoughts.

'I mean one minute you're insulting me and the next you're screaming about Elizabeth'

_Shit!_

'Elizabeth! Where is she Rodney is she here?'

Rodney looked at John with a worried expression on his face.

'Urm John, what—' he stopped as he saw John frantically look around the infirmary.

'Rodney! Where is she? We have to go back to get her NOW! She could be in serious trouble! The Ongarians, they lied to us. They drugged us and…where the hell are you going!' John put the glass to the side and made to get up but was quickly intercepted by Carson.

'Where d'ya think your goin son?'

'Elizabeth! Please Carson you have to find her!' He continued to struggle against Carson's grip but relented when a massive wave of dizziness overcame him.

_I'm gonna be sick…_

John laid his head back down and tried to fight off the darkness that was overcoming him.

'_**John Sheppard, I told you she will be punished. Don't bother looking for her…she won't be there for you to find'**_

'Liz'beth' he muttered. The last thing he heard was Rodney and Carson muttering to each other.

'Carson...who's Elizabeth?'

'Honestly Rodney, I have no idea'

**Evil cliff-hanger I know but don't kill me or you won't get more! Review please! First time I've written anything smut related so would like to know if it went well...do I continue using stuff like that or do I suck unbelievably at writing it? Honest comments...I won't seek revenge or anything!**


	5. Chapter 5

**AN: Urm...don't kill me? SO SORRY FOR THE DELAY! Really, really hectic life atm. But anyway, this one's done now and I plan to have the 6th chapter up soon...I actually mean that this time...maybe.. :P**

**But anyway, I want to say a huge thank you to all you reviewers who have been so encouraging; if it wasn't for you I wouldn't have gotten this chapter up at all but you guilted me into it, so thank you :P**

**A special thank you to lisabeth39 who has been reviewing on both fanfiction and command dynamics, offering great support on both so thanks :)**

**Also I realised (again), ERROR! I've been referring to Sheppard as 'Major' before but have changed that so yh...enjoy!**

'Weir!'

Elizabeth looked up in surprise, almost dropping her cargo with fright as the man walked up to her, whip ready in his hands.

She sighed slightly as she bent down to place the stone bricks on the floor at her feet.

As soon as she deposited the bricks she stood, barely supporting herself on her unsteady legs. She held her hands out in front of her, waiting to be bound.

'Good girl' remarked the man before he tightly tied her hands together.

She braced herself as she was roughly dragged forward, wondering briefly what they were going to do to her this time.

_I don't care_ she thought after a minute. The frightening thing was that she really didn't.

Elizabeth had been working in Atarus for at least a week and Atlantis had yet to make an appearance.

_Maybe they've given up...maybe they think I'm dead._

But a small part of her mind fought against that thought, knowing and trusting that her friends wouldn't give up on her and John that easily.

_John..._

That small hopeful part of her mind refused to give in because of John.

_He wouldn't want me like this; giving up. He'd want me to stay strong and positive. He'd want me to feel and care...not just give in to the pain._

But every time she tried to listen to that hopeful part of her mind, every time she came close to regaining some strength, something came along to ruin it; _John's not here, he never will be _countered the hopeless part of her mind. _He's dead _it continued to taunt.

Every day she fought this inner battle and every day the dark part of her mind grew stronger, more convincing.

_You're not going to escape Elizabeth, they've abandoned you. You're dead to them...just give up!_

She tried to fight the hopelessness and overwhelming despair, if not for her then for John, but it was the thought of him that also caused her to lose.

_There is no more John, he's dead. John is dead and there is nothing more to fight for...a life without him is no life for me._

She knew rationally that hope would keep her alive longer; it would keep her sane and strong. But she also knew that hope was now an illusion; if there was no John then there was no hope.

_I should have listened to him _she thought. _It's my fault he's dead. He's saved my life so many times and I can't listen to him for two seconds! He saved me and I repay him by killing him!_

It was that thought that plagued her dreams. The single thought of his undeserved demise that caused her to accept her circumstances she was in...her punishment.

_I killed him, I deserve death._

She clung to this thought as the man stripped her and bound her to a chair.

Through his beatings and rape it was this thought that kept her from fighting.

_I killed him, I should die. I must suffer..._

She held on to that thought as the pain became so unbearable that she blacked out.

xxxxxx

He lay there, staring up at the infirmary ceiling whilst thinking over his and Carson's earlier conversation.

_**Flashback**_

''_**Colonel? Good to see you awake again'**_

'_**Carson?'**_

_**John's vision blurred slightly before he was able to focus on Carson standing over him, worry written all across his face.**_

'_**How long?' asked John.**_

_**Carson reached for a nearby glass of water and helped John drink it.**_

'_**About five days' he replied as John began drinking...big mistake.**_

_**John choked as his eyes widened in disbelief. Spluttering, he tried to sit up, eventually doing so with help from Carson.**_

'_**Easy son' he said whilst patting John on the back.**_

'_**Carson, have you found Elizabeth?' he struggled through more coughing.**_

_**Carson just looked at John, studying him whilst trying to decide what to say.**_

_**John seeing the hesitation automatically assumed the worst.**_

'_**No, Carson where is she? Is she still alive? Please she can't be dead she can't!'**_

_**At this point he was fighting Carson to get out of bed, a futile attempt as he was barely strong enough to hold his own head up.**_

'_**Relax son or I'll have you sedated' Carson warned. John's pathetic attempts at getting up ceased immediately.**_

'_**Good, now tell me Colonel...who is this Elizabeth you keep mentioning?'**_

_**John stared at Carson whilst trying to figure out if he'd just heard correctly.**_

'_**...what?' he eventually replied.**_

'_**Elizabeth...who is she Colonel?' questioned Carson patiently.**_

**This isn't real it can't be!**

_**John wanted to believe his mind so much but knew he was hearing correctly.**_

'_**Urm you know...Elizabeth. As in Elizabeth Weir?'**_

_**Carson just stared, his eyebrow slightly raised.**_

'_**Elizabeth Weir being the leader of this expedition...our good friend Elizabeth?' John pressed further.**_

'_**Colonel, our expedition leader is Colonel Sumner...always has been' replied a very concerned Carson.**_

_**John's mouth opened to protest but no words came forth. He tried to comprehend the information for a minute until it finally hit him...he smiled.**_

'_**Good one Carson! Did Rodney put you up to that one? Coz I got to admit it's a good one! Completely had me there!'**_

_**John's face however fell and the concerned look on Carson's face magnified. John watched as Carson reached for his earpiece.**_

'_**Colonel Sumner this is Doctor Beckett, the Colonel is awake but he's sayin the most peculiar things. You might want to get down here'**_

_**John was about to argue but was swiftly cut short but a surprising voice.**_

'_**On my way, Sumner out'**_

_**John's mouth fell.**_

**That was Sumner...that was actually Sumner!**

'_**John!'**_

_**John quickly snapped his attention back to Beckett.**_

'_**Yeah?' he asked unsurely.**_

'_**I said I'm going to run some more scans. We've obviously missed something...'**_

**Yeah, Elizabeth **_**John grimly thought as he gave a slight nod towards Carson.**_

_**Flashback Over**_

John restlessly turned on his side as his frustration grew. All this time was being wasted on him when it should have been used to find Elizabeth.

'_Who's Elizabeth Weir?' _echoed Sumner's voice in his head.

Shortly after Beckett had summoned the Colonel to the infirmary, John had seen firsthand that Sumner was in fact alive. He had physically walked in looking as cold and stern as always. Hell he'd even given John a lecture about following the proper chain of command! There was no denying it, Sumner was alive and apparently the expedition leader from the beginning.

_Maybe an alternate reality? _John questioned himself, but gave up on the idea after a minute of confused thought.

_OK this stuff is way beyond me but it just doesn't feel like an alternate reality...this has something to do with the Ongarians. Elizabeth is real and I need to find her._

'Colonel Sheppard?' interrupted Beckett.

He sighed as Beckett walked towards him, his 'Doctor's mask' placed firmly on his face.

'Look Doc, I can tell there's something wrong so what is it?' John cut in before Beckett could speak.

Carson gave a weak smile before replying.

'I'm keeping you in Colonel, for how long I can't be sure. My understanding of your condition is limited at the moment but I promise you I'll—'

'Carson.' John swiftly interrupted. 'It's not your fault' he smiled to add reassurance. 'Just tell me what you know for now Doc'

Beckett sighed slightly before he began to recite what he knew.

'Your condition actually makes no sense to me whatsoever Colonel. Your dopamine levels suggest you should be in the severe stages of Schizophrenia'

Beckett paused before he continued, knowing his next words would not be easy for the Colonel to hear.

'One of the main symptoms of this condition, especially at this stage, is hallucinations. Now this is just an educated guess Colonel, but I think your friend Elizabeth is nothing more than a hallucination.' He studied John carefully, watching as he struggled to take in the new information.

'There's still the main issue of how rare it is for a man of your age to develop this condition. Not only that, but there has never been a sign of you having this in any of your medical scans, recent or otherwise. With your dopamine levels the way they are, this should have been detected by now. You should also be experiencing at least some of the negative symptoms as well as severe behavioural problems. But aside from that Colonel you're as healthy as a horse...the only concern is this Elizabeth person but even then, you seem like your usual self.'

John struggled with the news as he sat upright, noticing Beckett was looking at him, patiently waiting for him to take things in.

'So...what are you saying?' he finally managed.

'What I'm saying Colonel, is that you need to stay where I can monitor you. I'm relieving you of active duty and you are confined to the infirmary.'

John sat there, trying to wrap his head around the new situation. After a while and an intense inner battle he said the one thing he could.

'...no.'

Carson sighed, realising that any hope of an easy way out had just been shattered.

'Colonel I know this is-'

'No!' John repeated, this time more forcefully.

Carson watched as John summoned strength he wasn't supposed to have and got out of the bed.

'Colonel, I am ordering you to stand down!' Carson moved towards him only to be pushed back by John.

'She's real Carson I know she is! I'm not insane I swear! We were with the Ongarians and something happened, I was injured and she was taken away now Carson, we MUST find her...it could already be too late' he added quietly.

'Look Colonel, you are in no position to be mounting a rescue. Obviously I was wrong about the mood swings but I need you to shut up and sit down!' Carson yelled.

John froze in surprise at how un-Carson like Carson was being.

_He's hiding something_ John realised after the Doctor looked down at the floor. _Something isn't right; I'm no medical expert but something about this isn't adding up._

John made to move but stopped as realisation took over.

_Hang on...Rodney all caring earlier, Carson now...Ongarians...no Elizabeth...Sumner...Elizabeth...Ongarians..._John's mind suddenly became chaos.

_Shit! This isn't real. I'm still on the planet I must be!_ _They're doing this to me somehow!_

John suddenly shot forward, knocking Beckett to the floor. After a brief glance around the infirmary he exited, grabbing a knife-like instrument on the way out. _Scalpel _he randomly reminded himself.

John made his way to the Jumper Bay, being careful to stay unseen. However that didn't prove to be much of a problem for no one was around.

_Hang on, this is too easy...where is everyone?_

He pushed the thought aside for the mean time and focused solely on getting to the Jumper Bay.

_Not far now, just one more corridor..._

He reached the door and immediately halted as he came face to face with none other than Sumner.

'John Sheppard' he smirked. Then pain and nothingness as John was hit over the back of the head.

xxxxxx

John awoke to the sound of voices frantically nattering away about something.

'Wha?' he dumbly questioned, only to receive a kick to the stomach.

'Stop!' came a sudden voice.

'We need him conscious for this' it said again.

John was dragged off the floor and pulled to his feet, surprised to find himself in Atlantis' brig.

'What the hell is going on?' John demanded but received yet another hit to the stomach.

'I said, STOP!' shouted the voice again. John looked up in time to see the man who had been beating him fall to the floor, a knife protruding from his back.

'Such a _pitash!_' spat the voice again.

John stared in disbelief as a three foot something Ongarian made his way towards him.

_This midget just took down that six foot guard? What the-_

'John Sheppard of Atlantis. I must be honest; it is not an honour. More of a nuisance actually.'

John could do nothing except stand there with his mouth wide open from shock.

'You see...'continued the small Ongarian, 'I was sitting happily in my home, eating happily with my family when I suddenly and irritatingly enough, get a call regarding you. Now what was that abou—DONT LOOK AWAY! YOU KNOW IT'S DISRESPECTFUL TO LOOK AWAY WHEN YOU'RE BEING TALKED TO! GUARDS, BRING HIM!'

John just gaped further as he was dragged away.

_I'm a prisoner of an insane Ongarian midget...how the fuck did I get in this situation?_

John was dragged further into a small grey room with weird bits of machinery littered all round. In the middle sat a metal bed with restraints.

_Oh shit, these are never good in the films._

The guards forced John onto the bed, easily overpowering his struggles to get free.

When he was finally restrained, they stepped away to stand guard at the door. The small Ongarian sauntered towards the bed.

'Now, we will talk...LOOK AT ME!' he shouted in a voice so high pitched that John had to oblige for fear of his eardrums.

'Better' commented the Ongarian in his less pitched voice.

'Now, explain to me why you gave my scientists such trouble with the programme?' he waited for John to give him an answer.

'Urm...programme?'

'Stupid _mitvah_' muttered the Ongarian. Sighing he took a seat near John's bed and sat down.

'You were placed in a machine that simulated a virtual reality for you. You were meant to comply with it but your obsession with this...woman, got the better of you.'

'Elizabeth! Where is she?' John demanded as he suddenly remembered the reason for all of this.

'She better be OK or so help me I will KILL you!' he spat to the Ongarian who looked nothing but bored at the 'threat'.

'John Sheppard, you have and will continue to cause us great annoyance. Even from the start you somehow possessed the ability to connect with our minds. The council has decided to-'

'Hang on' John interrupted. 'You lot are telepathic?'

The Ongarian sighed in frustration.

'Yes, some of us are. You somehow connected with our link and discovered our plans for your female leader...I was going to interrogate you on how you did it but I doubt your stupidity allows you to know' he answered.

_Arrogant Bastard _muttered John's mind.

'I heard that' stated the Ongarian.

_Fuck you! Did you hear that? _John smirked in triumph when the Ongarian's face reflected that he had clearly heard the insult.

'You think you win?' asked the Ongarian after a moment. 'Well think again' he snarled as he stood up.

'As I was saying, the council has decided you are too much hassle to study. Instead, we will incorporate you into our society and use you as further punishment for your deceitful leader!'

Before John could question any of this, the Ongarian pulled a needle from his pocket and began to prep it for use.

_I hate needles..._a thought John regretted as he realised the Ongarian had heard him.

'Good to know' commented the Ongarian.

John tried to struggle against the restraints but knew he had no chance of escaping.

'What are you doing? What is that?'

The Ongarian merely smiled down at him whilst he continued to ready the syringe.

'I already said, you are going to provide further punishment for your leader. This...' he said as he lifted the syringe to the light '...this will erase you as a person; your memory will be wiped and replaced with one we created, one that is...how do we put this? Convinced that the female leader should be punished in the cruellest ways possible?'

He laughed as he heard the stream of curses emanating from John's mind.

'Our people will come for us!' John tried.

'No, they have been searching but I believe they will be giving up soon. You see, we staged your deaths. After we tranquilised you we took some blood and made replicas of your uniforms. Your friends are currently studying what they believe to be you and your leaders clothes...your blood added of course for authentication' He smiled as John continued to insult him silently.

'I knew you weren't to be trusted you bastard!' John was struggling so much against the restraints that the Ongarian showed a brief moment of panic when John's body lifted off the table.

However, one of the guards from the door came to hold him down and turn his head so his neck was exposed for the injection.

The Ongarians laughed as John became paralysed; the effects of the drug quickly kicking in.

All senses were lost and he could slowly feel his mind slipping away...

The last thing he heard was the Ongarian whispering in his ear;

'Goodbye John Sheppard...you are one of us now'

**In the real Atlantis...**

'You what!' exclaimed Rodney.

He hadn't slept properly since the death of Atlantis' leaders reached them. The whole city was in a state of mourning, all of them feeling like a part of them had been ripped away.

The news had come as a shock. When John and Elizabeth hadn't returned from the tour Ronon began to grow suspicious. He suggested they go looking for them despite not being allowed to leave their quarters. Teyla had agreed and she, Ronon and Rodney began their search.

However, as the made to exit the building a guard ran up to them holding the tattered remains of some clothes.

The realisation of who the uniforms had belonged to dawned quickly, particularly when John's dog tags were pulled into view.

Ronon went Ronon and pulled a gun on the servant. Teyla being who she was managed to quieten the angry warrior and convince him to lower his gun. Rodney had just stood there completely at a loss for words; something that very rarely happened.

They had spoken to the council members on the tour with them. The Chief told them a native wild animal had attacked them after the pair had digressed from the others. By the time they were reached it was too late.

Naturally further study was made; the clothes were taken back and analysed whilst Ronon and Teyla led an investigation. However, the naturally suspicious nature of the Ongarian people made the whole thing a lot of trouble.

It was for this reason that they were ordered to stop the investigation. Stargate Command believed that the use of resources being put into this and the risk of angering a technologically advanced society was too great.

The city had protested, buying them a little more time however, that time was now coming to an end. The SGC had just messaged in to say the search must be stopped.

'You heard me Doctor McKay, the evidence is conclusive. Doctor Beckett has submitted his report to me; the uniforms and blood found on them match that of Doctor Weir and Colonel Sheppard. No trace of them has been found all week and the Ongarians are beginning to lose patience; there is nothing else to it. It's time to move on. Atlantis cannot function without qualified leaders'

McKay glanced briefly over to Carson who was giving him an apologetic look.

'Fine.' Rodney replied eventually before storming out of the control room.

Ronon glanced over to Teyla for guidance on what to do.

'Leave him' she said after a while. 'We have to let him mourn on his own. For now, we have a lot of preparations for their memorial service.'

'Ay, not to mention the replacements to sort out' added Carson bitterly.

'Yh, I don't get that; how can we just replace them?' asked Ronon.

Carson smiled at the tall Satedan.

'We have to find suitable replacements by order of the SGC. They don't mean any disrespect but Atlantis needs qualified leaders for both the expedition and the military. Don't worry though, it doesn't mean we have to forget them.' He added as an attempt to try and lift the spirits of his two alien friends.

Ronon just nodded before he walked out. Teyla on the other hand smiled slightly at Doctor Beckett.

After a while she simply hugged him, not knowing what else to do or say. With that she exited the room.

Carson looked down at his feet whilst he wondered what would happen now. His words had shown more confidence than he felt; he wasn't coping too well with the loss of two of his greatest friends.

He sighed as he turned to Chuck who was sitting not far in front of him, looking equally as solemn.

'Chuck? Call in our teams...the search is over'

**I can't remember if Chuck is actually in the second season but I don't care because he's awesome xD.**

**No offence meant about the midget thing by the way; just in case.**

**Review please! Let me know how I'm doing...as I said, I will try to update sooner but I'm back to school soon; 6****th**** form is an early start (funfunfun!) But I have some evil ideas for the next chapters...possibly a bit dark but that's what I'm aiming for :P**


	6. Chapter 6

**Disclaimer: only the plot is mine**

**AN: Wow, my last update was longer than I realised. Sorry about that; back to school and tonnes of work. I actually have 10 pieces (I'm doing 5 subjects but I still manage to get 10!) of work to do so this chapter is kind of short. More explanations on that at the bottom though…for now, enjoy!**

**Spoilers: None**

**Warnings: None**

'Update Oran'

Oran turned to greet the Chief.

'Sir, we are making good progress; the new personality is swiftly overwriting his. We predict an hour until we can send him to the working grounds'

The Chief let out a quiet chuckle as he thought of what lay ahead for the good doctor Weir.

'Excellent Oran, report to the council when you are finished. They wish to repay you for you brilliant mind'

Oran smiled and bowed his head respectively as the Chief walked out of the room. He then turned back towards the man lying on the bed behind him.

'John Sheppard' he sneered. 'Just wait and see what I have in store for you' he said as he picked up a needle from a nearby tray. He was stopped, however, by a hand on his arm.

'Sir, with all do respect do you think that's wise? He may regain control…not to mention you haven't even _told_ the council!'

Oran sighed at his young assistant.

'How many times have I told you? He won't be able to regain any control, he is just going to be a presence within…just to observe. And I believe the council will be quite pleased that it won't just be Doctor Weir suffering'.

Oran smiled to himself as he pulled away from his assistant and began to prep the needle. His assistant just stood there whilst silently protesting. He knew it was a bad idea but he also knew better than to question her master further.

'Run further scans on his brain Mira, tell me when two patterns can be detected'.

Mira nodded and reluctantly moved to run the scans.

'I hope this works sir' she said quietly. 'You're the greatest person I know'

Oran raised his head to look at her. He took in her slumped posture, finally realising just how much this was worrying her.

'If this doesn't work Mira then you don't need to accept punishment with me' he said after a while.

She replied without hesitation.

'No. If this doesn't work and they find out then I accept punishment with you. It was, after all, I who developed the drug'

Oran smiled at her fondly. 'Yes, and a fine job you did of it Mira. It _will _work, I promise you' and with that he left the room.

xxxxxx

'Doctor McKay'

_I hate you_ was Rodney's automatic thought as he entered the briefing room to find Mr Woolsey sitting at the head of the table.

'How have you been?' asked Woolsey once McKay had settled himself.

'Fine thanks.' was Rodney's automated reply.

Woolsey sighed as he realised yet another day was to go by with Atlantis' smartest Doctor giving him the cold shoulder. What bothered him more was that it wasn't just Rodney. The entire personnel of Atlantis, military and civilian alike, avoided him where possible. A few such as Carson were slightly more civil but even then it was obvious how forced it was.

_Still, that may all change by today_ he thought to himself, making sure to nod to Teyla, Ronon and Carson as they walked in.

Teyla nodded back politely as was her custom. Carson gave a small smile that didn't even come close to reaching his eyes. And Ronon…well, Ronon was Ronon.

Woolsey waited for everyone to organise themselves. Once all seated, he gave a slight cough to catch McKay's attention who, eventually, looked up.

'Now, none of you have a clue why you're here. What I am about to say will stay off-record and most certainly away from Stargate Command is that clear?'

If Rodney's attention wasn't caught before it most certainly was now. Everyone looked at each other, questioning and confuse expressions covering their faces. After a round of nods and muttered 'yes sir's', Woolsey continued.

'Ever since this city lost its leaders, morale on this base has been appalling. It's been so appalling that I am finding it extremely difficult to maintain command here. To be honest, I couldn't be more disappointed. With you lot especially.' He paused before he said his next words, making sure he didn't raise his voice.

'You are commanding officers of your respective departments and as such I expect you to act with a certain air of professionalism'

He paused to take in the shocked looks aimed in his direction. When he saw the embarrassment on McKay's face he had to try extremely hard to hold in a laugh.

'I should have reported you all to Stargate Command a long time ago but I didn't. I chose to give you some time to adapt. I tried to give you time to accept Doctor Wier and Colonel Sheppard's deaths but you just took advantage of that. This is your last chance. If anyone questions the orders I am about to give you… _anyone_' he glared at McKay to make sure he knew that included him as well. 'then you will be out of here before you can say wormhole is that clear?'

Everyone nodded stiffly as they waited to hear their dreaded orders. After a long pause Woolsey finally smiled.

'I am ordering you to continue the search for Doctor Weir and Colonel Sheppard'

**I love my cliffhangers! xD I started writing this but realised I actually have to get some work done. If I can I'll update it again today, maybe tomorrow. But from now on updates will most likely come on the weekends. **

**And I still like reviews! :D**


	7. Chapter 7

**OK THIS IS A REDO OF CHAPTER 7...a few minor adjustments to it for later purposes. For those of you who read it you don't HAVE to read it again...a skim read might help but it's not vital. I was just having an OCD moment :P Anyway, I'm doing bugger all today so next chapter should be up soon!**

**Spoilers: None**

**Warnings: None**

**I'll do a quick re-cap: John has undergone this scientific experiment that will effectively wipe his personality and replace it with a programmed false one. There was a risk involved; that he might regain his personality but the scientist (Oran) is convinced it won't happen. Meanwhile, in Atlantis, Woolsey has secretly resumed the search for the two missing leaders, convinced that they are still out there. **

**And now the conclusion…or the next chapter at least.**

'What is your name?'

'Tyran'

'What is your occupation?'

'I am a guard at the Atarus working grounds'

'And your loyalties lie where?'

'I am loyal to you my Chief. I serve Ongaria and protect its people from the brutal savages that have rightfully earned their place in our prisons'

The Chief smirked as he saw Tyran kneeling before him and the rest of the sneering Ongarian council.

'Good, Tyran. I am proud of your progress. Even without your memories you have done well. Now tell me, what has Oran told you about your new assignment?'

'Nothing my Chief. He told me that I should wait until you felt I was ready'

The Chief nodded then indicated for Tyran to sit.

'You are ready'

Tyran rose from his kneeling position and moved towards the seat that sat in the middle of the room. He noticed the rest of the council shift forwards in their chairs slightly as he sat.

'You know of Atlantis?' asked the Chief once Tyran had sat down.

'No'

'Atlantis is the city of the Ancients.' began the Chief. 'It has recently been inhabited with a scavenger race of humans from a distant planet. In the short while they have been in this galaxy, they have managed to reawaken the Wraith. Do you remember the Wraith?'

Tyran nodded.

'The Wraith have awoken too early. Thousands are dying and it is all because of those humans. Their leader is none other than a female who does not even possess the Ancient gene. She is the one who you will be in charge of in the working grounds.'

Tyran hung on to every word, anger filling him as the Chief continued to describe the treacherous acts of the humans.

'What do you require me to do?' he asked once the Chief finished talking.

A snicker circulated the room after Tyran asked the question.

'We would like you to punish the female. You see, you look a lot like her beloved John Sheppard; her late second in command and partner. She is confused and delusional enough to think you are him. You have the potential to deliver the greatest damage to her; a great favour to the true residents of this galaxy and a personal request of our masters. The wraith high council want this of us and Tyran, I'm sure you remember why we must remain on their good side?'

Tyran nodded slightly as he processed this new information.

'Of course my Chief. But what of the male? Her second in command; John Sheppard?'

More snickering from the council, this time slightly louder.

'We captured him the same way we did her but, shamefully, he was weaker than her; he did not survive.'

Tyran smiled slightly at this news. 'That is a shame, I believe we could have had such fun with him too.'

Tyran looked on curiously as full-out laughter overtook the room.

_They're hiding something from me_ he thought as he put on a smile for their benefit.

'Yes well, these humans are frail.' replied the Chief eventually.

Tyran nodded and sat patiently as he waited for the hall to quieten down. After a minute or two, the Chief began to speak again.

'Tyran, if you do not feel ready for this we will understand. You are still recovering from your accident and you will most likely never regain your memories again. This is a lot to take in we understa- '

'No my Chief I am fine. I have heard many stories of my past; I used to be the best at my job and I intend to reclaim my old standards. Do you require anything else from the female? Any information?' Tyran asked, careful to hold the chief's gaze.

The chief smiled and sent an approving nod in Tyran's direction. 'The main objective is for her to lose all hope; it would be a rather beneficial punishment for her crimes. However, now that you mention it…' Tyran straightened his posture in his seat as the chief leaned forward slightly in his chair.

'…any information you can get from her regarding Atlantis' weapons and defences may prove useful to our masters. I won't deny that the task will be challenging and probably futile, but…'

'I will learn all information I can my chief' Tyran finished. He waited patiently as the hall once again was filled with quiet snickers of the council members.

'I am glad we can trust you with such a task. Now go, do us proud Tyran' the chief finally said.

'Yes my Chief' replied Tyran as he got up from his chair.

'You will leave tomorrow. Report to Oran's lab for a check-up after your training. Dismissed'

Tyran bowed his head respectfully before he exited the room. Once he was out, he thought back to his assignment. He thought back to how angry he felt when the Chief described all that the humans had done to the galaxy. He thought of how happy he was when he discovered John Sheppard had died. He also remembered feeling annoyance shortly after because he had missed his chance to make the human male pay.

_At least I can make the female pay…that might be more fun._ He smirked as he thought of all the things he would do, all the things he could use to his advantage.

He reached his quarters and walked straight through to the bathroom. He stopped in front of the mirror and stared into it, not quite sure why or what he was doing.

_**Look at me**_ he suddenly heard from no where. He looked around and shook his head after realising no one was there.

_Probably just tired…_ Yet he could not seem to turn away from his reflection.

_**Look at me **_came the voice again.

Tyran moved closer to the mirror so he could study himself better, somehow knowing this is what the voice meant.

_I look the same. Same green eyes, same uncontrollable hair…same boyish features_. He smiled as he thought the last one to himself. _The women love me for it._

_**You already have a woman; you already love someone **_came that voice again.

Tyran continued to stare into the mirror, a small tendril of fear slowly snaking its way across his features.

'Who are you?' he whispered to no one.

He waited a few minutes to hear a reply. When none came, he shook his head and turned on the tap to fill the sink.

'It's probably the medication. I'll talk to Oran tomorrow about it' he mumbled to himself.

Tyran finished up in the bathroom and made his way over to the bed. He decided to forgo taking his medicine, convinced that it was the cause for him hearing voices. Instead, he decided to do what he always did before bed; dwell on his dreams. Tyran had been getting strange dreams since the accident. Oran said it was merely his sub-conscious trying to make sense of certain events and that he should not ponder them too much. Even so, Tyran couldn't help but think there was much more to it. Usually the dreams entailed spaceships, a floating city and weird bullet-proof vests. But recently, they had been showing a woman. Who this person was, he did not know but he couldn't help but feel uneasy when he thought about her. He needed to remember. He knew he must, he knew she was real. But at the same time he knew it would put him or someone in danger if he found out.

These thoughts continued to circulate in his head until eventually he fell asleep, his dreams filled by with a curly brown haired woman and her bright green eyes.

**Back in the hall with the council…**

'You have done well Oran' praised the Chief as Oran stepped out from the shadows.

'Yes sir, but I cannot take all the credit. Mira helped me significantly' he smiled at the figure of the woman who followed close behind him.

The Chief nodded his acknowledgement of her presence before once again turning to Oran, this time lowering his voice.

'If anything goes wrong, you will be held responsible is that clear?' he warned.

Oran silently reached behind to reassuringly hold Mira's hand.

'Yes sir' he replied as both he and Mira bowed their heads low, waiting to be told to raise them again.

The Chief studied them for a minute before dismissing them.

_I hope for all our sakes you succeeded in wiping Sheppard's memory _he thought to himself. _If he ever regains it and finds out what we did…he'll kill us all._

**Over to Atlantis…**

'Hey Carson, what did you need?' asked Rodney as he cheerfully walked in the infirmary.

Ever since Woolsey had made his decision public, morale in the city had significantly increased. Everyone was working towards getting their two leaders back. McKay had been improving Atlantis' technology, making sure it was all working at its best. Teyla was offworld with Lorne's and various other teams, trying to gain allies and find information on the Ongarians. Ronon took Lorne's place as military leader and devised a plan with Woolsey that would be used if diplomatic methods failed, which Woolsey was pretty sure they would. Beckett had been running every scan he could think of on the remains of the clothes they had received. He had almost admitted defeat when one of the teams brought back some alien tech that enabled them to run at least a dozen new scans. Rodney had sent a team to install it which meant either Beckett had broken it already or he had fond something. Rodney was really hoping for the latter.

'Hi Rodney. This technology is fascinating. I've run so many scans and more can still be run. It's great for-'

'OK Carson, as much as I love this, I already know how it works and I'm kinda busy with the jumpers right now so if you don't-'

'Rodney. We found something. I've just ordered another scan to double check but I think we're onto something'. Beckett smiled as Rodney's face lit up.

'How do you mean 'found something' like what? Something big?'

'I mean ma friend, if the test comes back positive then there is a very good chance they are alive'. Rodney practically beamed.

'Doctor Beckett! It's a positive they're alive! THEY'RE ALIVE!' screamed a nurse as she ran up and practically threw the results at Beckett.

Rodney laughed as he threw an arm around a stunned but happy Beckett.

'I'll go tell Woolsey!' he said as he practically ran down the hall, leaving a room full of screaming nurses behind.

_You lucky guy Sheppard_ thought Rodney as he darted inside the transporter. _You're still out there with Elizabeth and we __**will**__ bring you home._

**So as usual, reviews make me happy! :) I'd like some input on the next chapter. It has the potential to be quite dark. It's not too hard to guess some of the things that could happen but I'll hint by saying I'm going for anything emotionally traumatic to both John and Elizabeth. You guys OK with that or do you need a less traumatizing version? Feedback please: the more I get the quicker I can write. Might have Sunday to do this so if I get enough by then you could get another chapter!**


	8. Chapter 8

**AN: Woo next chapter! Thanks for all reviews and I'm sorry this one took so long. I might even be able to get the next chapter up today but for now, I'm going to watch some sg1 and sga…it's been a while since I did that and my brain is hurting from overuse of writing :P**

**No spoilers and content is pretty much the same dark angsty stuff that goes on in this story.**

**Enjoy :)**

'So Tyran…are you ready?'

Tyran winced as Oran pierced his skin with a needle.

'Yes Doctor I'm ready' he replied as he held pressure to the small puncture in his arm.

Oran stepped back to study the man in front of him. _I hope you're ready _he thought. _For both mine and Mira's sake._

'OK, before I let you leave, any concerns? Any aches or pains? Anything at all?'

Tyran continued to look at his arm as he considered his answer.

_Do I tell him? Or do I just ignore it. _But after a quick internal debate he decided against it and smiled as he lifted his head to face Oran.

'No I'm fine. Minor aches but I think that's just my body adjusting to moving again. After all, I have been out of it for a while'

Tyran continued to hold Oran's piercing gaze, afraid if he looked away then all would be revealed.

_He must not know. If he finds out I won't be able to do this mission!_

Tyran gave an internal sigh of relief as Oran briefly nodded before looking back at some notes he'd been taking.

'OK then, I guess good luck and have fun is all that's left then. You may go Tyran. Bay 3.'

Tyran hopped down off of the bed and slapped Oran on the shoulder.

'Thanks Doc.' Tyran called as he practically bounced out of the room.

Oran could do nothing but stare after him as he processed his patient's strange actions and words.

_Doc? Where did that come from?_

**In Atlantis…**

Teyla entered the conference room with a purposeful smile on her face, covering the dread of revealing the news she knew had to be shared.

'Ah Teyla. Welcome home' came Woolsey's greeting as she approached her seat.

She politely nodded in his direction as she sat down, also making sure to acknowledge the others that sat around the table. When her eyes met Lorne's she held his gaze, silently asking permission that she be the one to break the news they had both learned whilst on their latest mission. He gave a subtle nod in reply that was missed by everyone else.

'So, now that we're all back, what news do you have for us?' asked Woolsey, glancing reflexively over to Lorne.

'Well sir, the Ongarian's are not as widely known as we hoped and those that know of them fear them. We have managed to gain some allies but there was some information we learned on our latest mission that was somewhat…troubling.' Began Lorne, nodding everyone's attention over to Teyla when he had finished.

When Teyla was sure she had everyone's attention she began to speak.

'The Linarans were the inhabitants of the latest planet we visited. Their hatred for the wraith is strangely minute when compared with their hatred for wraith worshippers. It is Linaran law that if any man, woman or even child were to speak of wraith worshippers in good terms, they would be imprisoned and then most likely executed. They dispatch hunting parties through the stargate to hunt down wraith worshippers. They even follow some worshippers to gain information on what the wraith are doing. In many respects their workings are similar to those of the Genii.'

'Teyla, sorry to interrupt but if my memory serves correct, the Linarans wanted nothing to do with us, even after we offered them better methods to fight the wraith and wraith worshippers' stated Woolsey.

Teyla nodded in his direction, taking a moment to figure out how to phrase her next words.

'Yes you are correct in regards to that. But the Linarans were extremely eager to help our cause…that is once we mentioned the Ongarians'

Teyla noticed as everyone suddenly seemed to focus, their faces all trying to work out the implications of her words. Rodney was the first to get there.

'Wait. So what you're saying is that the Ongarians are wraith worshippers? We left John and Elizabeth in the hands of wraith worshippers?' came Rodney's outburst.

Teyla smiled sympathetically at Rodney's unbelieving face.

'I am afraid it gets worse. The Ongarians are the Linaran's greatest enemy because they are the biggest, most loyal wraith worshippers. According the Linaran chief, the Ongarians and Linarans were once a united people. But with the reawakening of the wraith and the Ancient's abandoning of Atlantis they began to divide. The Linarans were determined to fight the war against the wraith until none of them remained whereas the Ongarians wished to live peacefully, even if that meant they had to serve the wraith.'

Teyla took a deep breath in before she continued.

'The Linaran chief said he would be honoured to fight with us, but he also revealed some disturbing information. Their latest hunting party intercepted communications between the Ongarians and the wraith. According to the spies, both Elizabeth and Colonel Sheppard are alive'

She paused as the room's inhabitants' faces lit up, all except Lorne who merely gave her an encouraging, if forced smile.

Once everyone had focused back on Teyla she looked straight at Woolsey.

'But as I stated, the information received was disturbing. Both John and Elizabeth are alive, however, it appears Elizabeth is being held accountable for the awakening of the wraith and the theft of the Ancient City. The wraith merely wanted Atlantis' leaders captured but they gave permission to the Ongarians to do what they wish. Elizabeth is currently being held in a prison and she…she is not doing well.' replied Teyla as she tried to keep her voice steady.

'According to the Linaran chief, the two peoples once shared a telepathic link. It appeared that, somehow, Colonel Sheppard was able to use this link. He is currently involved in some kind of experiment.'

Pausing once more, she glanced at Lorne as if to try and summon the courage from him to say what they both knew was the worst bit.

'Another message was intercepted a few hours ago, just before we left. It stated that John was being shipped off to the Atarus working grounds; where Elizabeth is being held. John does not know who he is; the experiment has somehow altered his memories. What we are certain of is that John is being used to punish Elizabeth. The Linarans intercepted an order from the Chief to John, whom he referred to as Tyran. This order was to punish and then kill Elizabeth.

She paused, plucking the courage to glance at the faces of everyone sitting around the table. Carson looked worried, his brain no doubt trying to work out potential damage. Rodney looked as if he might pass out. Ronon looked about ready to kill someone and Woolsey looked downright disgusted.

'Thank you Teyla' he replied in a quiet tone. 'This information will help us greatly.' He nodded slightly as if to reassure himself of something.

Woolsey looked up at Ronon who was glaring right back; a look of understanding passing between the two men.

'Ronon, begin assembling the troops. Take Major Lorne with you and explain on the way.'

The two said men stood and nodded before leaving the room.

'Doctor McKay, I want an update on all the systems we will be using ASAP. Then when you're done get suited up and meet Ronon and Major Lorne in the Jumper bay.'

'Yes sir' came Rodney's startling reply before he practically ran for the door.

'Teyla, I understand you may be tired but-'

'I will go and bring the allied leaders' she smiled slightly as Woolsey nodded her dismissal.

_Now, to Beckett_ he thought to himself.

'Doctor Beckett, please assemble a medical team and have them suited up as well and ready to leave at 18:00. We don't know how we'll find them so best be prepared for the worse' Woolsey sighed.

Carson nodded in understanding. 'I'll do ma best' he said before leaving his seat to go to the infirmary.

Woolsey wearily rubbed his eyes before getting up to check Rodney's progress in the control room.

'All systems are ready and waiting' was the enthusiastic answer as he approached the catwalk, having to move slightly in order to avoid an excited Rodney running into him.

'Thank you Rodney. Ronon and Major Lorne are in the Jumper Bay waiting for you. Good luck.'

Rodney nodded briefly as he handed a data pad over to one of the technicians. He then turned to face Woolsey and offered out his hand. Woolsey shook it, shock evident all over his face. He then watched as the usually self-absorbed scientist ran out of the room and to the jumper bay.

**The Atarus Working grounds…**

_**Remember who you are…**_

_I am Tyran._

_**No, you are not Tyran. Tyran is Ongarian; we are not Ongarian. We are human…Who am I?**_

The voice was persistent, a silent headache that would not leave Tyran alone. It'd been worse when he boarded the ship. The chief had seen him off at Bay 3 and from there was a three hour trip to the working grounds. Tyran estimated a good two hours had passed but he could not be sure. Either way, it felt a lot longer.

The voice had not stopped bothering him; it was constantly there and it grew stronger with every passing minute.

_**Who are you?**_it continued to insist.

'Go away!' Tyra shouted as he pressed his hands to his head in some futile attempt to quieten the voice within. It seemed to work for a while but then the voice replied.

_**John Sheppard.**_

Tyran stared in shock, trying to figure out what was happening. Perhaps sensing a weakness from the confused mess, the voice continued.

_**You are John Sheppard. I am John Sheppard. They changed you somehow. You are NOT Tyran. We are John Sheppard.**_

'NO! GO AWAY GO AWAY GO AWAY! John Sheppard was human scum but he is DEAD! I am on my way to take revenge on the other human; the female scum. Revenge is the Ongarian's and I will do it for my masters. I am NOT John Sheppard!'

Tyran smiled as he felt the voice suddenly lose control, his mind becoming clear once again.

_Hate, I must keep hating. It fears that power that is why it retreats. I must not let it win; focus on my revenge._

He continued the mantra until he arrived at the working grounds. The thought of revenge gave him strength as he was lead through the grounds to a cell.

He waited as the door was opened. He could hear screams inside, screams that both horrified him and satiated him. He realised the voice within him was fighting him but he focused on the screams, knowing they came from John Sheppard's woman. He focused on the thought of revenge and how he would achieve it. He thought of how he would make her scream.

The voice within continued to try and fight but Tyran knew it was losing hope as he allowed images of his revenge to flood his mind.

By the time the guard opened the door the voice was heard no more. He stepped in, a victorious smile plastered clearly on his face as he gazed down at the thin, bleeding woman lying on the floor, the dirt on her cheeks making her tear tracks clearly visible.

Tyran walked in, giving the guard an appreciative nod as he moved to exit the room.

He knelt down so she would be able to see him when she opened her eyes. He waited patiently, knowing that just this simple action would in itself cause her so much damage.

Eventually she opened her eyes. Confusion evident on her face.

'John?' she almost whispered in disbelief.

He smiled at her, a cold heartless smile that promised nothing but pain to her. He pulled her by the arms and pinned her to the nearest wall, relishing the fear and pain that was so evident in her eyes.

He leaned in close until his nose barely touched hers.

'My name is Tyran' he whispered. 'John Sheppard is dead'

**DON'T KILL ME! I did take all your feedback on board don't worry, it isn't as bad as it seems. I was planning to post this and the next chapter together but as I said, I've been writing/typing all morning and my brain is pretty much goo right now. It will probably be up by tonight or tomorrow morning. Thanks for reviews and keep em coming :)**


	9. Chapter 9

**So this was supposed to be one long, final chapter but figured I kept you waiting long enough so here's a quick bit to keep you going. The next one will probably be the last one...or possibly the one after that. Either way, thank you for all the lovely reviews and thank you for sticking with the story...even though I often don't keep to the publishing deadlines :P**

**Warnings: abuse/violence of sorts...to be honest if you're bothered by it then I don't think you wouldn't have made it this far anyway :P**

"John…please…"

Tyran moved his mouth to Elizabeth's, capturing her in a forceful kiss that would surely leave her lips bruised. When he released her, he grabbed the back of her hair and forced her to look at him.

"Sheppard is dead lady. He is never coming back. You are alone" he taunted further, to which he gleefully received a scared whimper.

"No! John, you are John! Please come back to me" she pleaded desperately, her hand freeing itself to rest against his cheek.

Tyran froze at the sudden and somehow familiar contact. _What is this? Why am I feeling this?_

_**Move away Tyran…**_ came a weak but threatening reply from within.

Tyran smirked as he felt the voice try to gain power. Turning back to Elizabeth he smiled once more.

"You're right. I am Sheppard…but I don't want you anymore you good for nothing-"

"NO!"

Tyran was too shocked by the sudden outburst to realise she'd thrown him to the ground and was currently climbing on top of him, clawing at any part of his body she could reach in the process.

He struggled to fight her off, but just as suddenly as it started, Elizabeth ran out of energy and collapsed on top of him, quietly repeating John's name.

Tyran took the opportunity to flip her over and pin her with his superior body weight.

"I'm gonna make you regret that" he whispered, venom lacing his voice.

Elizabeth looked up to capture his green eyes with hers. Tyran was shocked with what he saw in them; not fear, but hurt and…

"I love you John" she whispered before closing her eyes, willing that familiar numbness to overtake her body.

"I love you John. I know you're in there so please come back to me. I need you…please"

Tyran screamed as he felt something ram into the side of his head, knocking him clear off Elizabeth.

He stared in bewilderment as his left arm raised on its own accord, fisting as if getting ready to punch again.

Tyran used his right arm to intercept another blow to the head. He was vaguely aware of the gasped "John" that escaped Elizabeth's lips from the floor.

_Damn you Sheppard. This is MY body now!_

"No Tyran, it's not."

Tyran recoiled as yet another more forceful blow hit him squarely on the nose. His scream barely covered the sickening crunch that followed.

He tried to speak but was horrified when he realised he couldn't.

_What have you done to me?_

"I have taken back what is mine."

**Atlantis…**

"OK people listen up!"

Rodney waited until all conversation in the jumper bay had ceased. It had been an hour since their meeting and during that time, almost half the base had gathered in the jumper bay to await the final run-through and the long-awaited mission 'go-ahead'.

"OK, we'll go through this quickly so we can actually get on with it. Teyla's team will dispatch first and distract the council on the surface. We've developed some transmitters given by one of our allies to transmit data up to Team 2, who, may I remind you, will remain cloaked. Everyone with me so far?"

A murmur of yes' swept through the room.

_Good_ thought Rodney. _We're getting somewhere._

"Now, Teams 3, 4 and 5 will be circling the surrounding space and keeping an eye out for any Wraith or Ongarian activity. The Linarans have also put forward two of their battle ships to back us up. Again, _cloaked ships._"

Rodney took a brief moment to nod in the direction of the Linaran leader.

_OK, now the hard part…_

"Team 1 will consist of Ronon, Lorne, Beckett and a small medical team, me plus 5 other Linaran soldiers. Now, I need to stress to you Lanteans… DO NOT KILL THE CHIEF."

Rodney pointedly looked at Ronon who merely raised an eyebrow in response.

"As much as we want to, this is part of the deal with the Linarans; the Ongarian Chief is theirs for the taking is that clear?"

Once again a series of muttered yes' echoed in the small bay.

"Ok so…Team 1 will be on standby to await any information on the whereabouts of Colonel Sheppard and Elizabeth. Once Team 2 detects their approximate position, Team 1 will enter the atmosphere to find them and bring them back. Just remember, the siren will sound when the atmosphere is breached. Team 1 will be on the planet and the rest of you need to assume your battle-plan positions is that clear?"

A stronger reply of 'yes sirs!' sounded in the room at this.

Rodney nodded in approval before continuing.

"Our Tirreten allies have provided us with a few transportation devices. As soon as Team 1 get a lock, we'll beam them aboard. Only when we clear the atmosphere do the rest of you, save for the Linarans, leave."

Rodney took a slow deep breath as a wave of apprehension suddenly encompassed the room.

_OK, we can do this…we'll do this._

"I have to say, I will be sad to say goodbye to this position" came the sudden voice of a nearby Woolsey. He stepped through the crowd to stand with Rodney on the platform.

"It was a bumpy start, but, it has been an honour to work with such dedicated people. I know the risk of the SGC finding us out has been strenuous on each and every one of you. But, you'll be pleased to know that when they get here for the inquiry, you will already be on your way home…with your two leaders."

Woolsey looked down at the crowd of anxious onlookers, pride evident on his face.

"God speed people. You have a go"

**So yeah, reviews please! I know this chapter was semi-pointless but hey, it gave you something to read. I've written some of the next chapter but not sure when it'll actually be up...shouldn't be too long though. I have pretty bad insomnia but writing fics has proved more fun than counting metaphorical sheep (which really sucks btw and is an actual therapy technique O.o) Anywho, until next time! :)**


	10. Chapter 10

**Woo finally updated. I was planning to fit everything into one chapter but was taking too long. This way you at least get something to read.**

**Thank you all for reviewing and reading. Much appreciated and I will try to update before mid-May, which is when my exams are *PAINIC!***

**NB: So far on **_**Love through Pain,**_** John/Tyran has reached the working grounds and is currently interrogating Elizabeth. John's persona has (predictably: P) started fighting back for control. Atlantis has a plan in place to get their leaders back.**

**Also, for later reference, the Atlantis plan was basically few jumpers and their ally ships (Linarans) in space to fight off the Ongarians and wraith (Ongarians are wraith-worshippers) and then Teyla's team is on the Ongarian planet as a distraction for Ongarian council and they were also going to do some sabotage work. Finally, Rodney, Beckett, Ronon and a few others are on a jumper to retrieve the two lost leaders... the ^.^.^. are basically signifying the transitions from John/Elizabeth scenes to the Atlantis rescue scenes.**

_Sheppard…you must relent…._

"No…"

"John."

_Give in Sheppard…you are one of us now, you must let go…NOW!_

"NO!"

John blindly grabbed in front of him and squeezed when his hand made contact with something.

"John- you're hur-ting…me…"

John's eyes snapped open at the sound of the familiar voice.

"…Elizabeth!"

Elizabeth fell back against a nearby wall, clutching at her throat as she tried to gasp for air.

"Elizabeth!"

John's head swam as he tried to lift it from the grubby floor, desperately trying to move over to the now sobbing Elizabeth.

"Liz…beth"

He fought the blackness that was threatening to overcome him, pushing his aching body in the direction of Elizabeth.

Finally, he reached her. He repositioned himself so his back was against the wall and pulled her towards his chest, noting with anger how fragile and thin she felt.

Elizabeth's gasping began to subside, leaving only the sound of soft sobbing in its place.

John lightly lifted her chin so she looked at him, cursing slightly when he saw the numerous injuries along her head. He turned her face gently to try and examine the rest of it, slightly worried at the glazed look that clouded her usually bright eyes.

"Lizabeth" he gently whispered to her.

She gave no sign that she had heard him.

"Elizabeth it's me. I'm back. It's me John. Tyran is gone and I promise you that no one will hurt you again I swear. I'm here now…"

John trailed off as a tear escaped and ran slowly down her cheek.

He gently used his thumb to wipe it away, noticing how she flinched slightly at his touch.

"Lizabeth, look at me. Please just look at me"

He waited patiently until she eventually turned her gaze towards him. But he wasn't ready for what he saw.

Her eyes were brimming with tears, pain and fear clearly etched in her gaze. Her long and drawn-out suffering had left a clear mark for all to see.

"God Elizabeth I'm sorry, I'm _so_ so sorry I…" John trailed off as tears began to fill his own eyes.

_God dammit Sheppard man up!_ He internally berated himself. But deep down he knew it didn't matter. He'd caused her, whether voluntary of not, so much pain. Pain which she was not going to forget any time soon…if ever.

_You should have fought harder John. You should have saved her sooner!_

He was surprised to feel a soft, small hand against his cheek; the thumb gently passing over his lower lip.

"Don't be sorry John. It wasn't you"

John gazed down into her still tear-filled eyes, glad to see some other emotion now taking over her fear; love.

"I love you" he whispered after a while, feeling that nothing else could really be said.

She smiled up at him as he reached to take the hand on his face in his. She watched as he placed her palm against his cheek and turned in to kiss her palm.

'I love you so much Elizabeth and I am so sorry I wasn't here for you sooner-'

'John. Stop. You're here now and that's all I care about.' She cupped his face in both her hands, making him meet her eyes as she tried to get the message across to him. She moved her thumb to wipe away the tears that had begun to fall down his face.

'John, I love you. You know I've loved you for a while, just like I know you have loved me too. It was you that I kept with me throughout all of this so yes, you have been there for me. Maybe not physically, but it was just as good'

Elizabeth leant forward and kissed him softly, being wary of both their injuries to try and prevent them from any more pain.

The kiss was soft and filled with promises for a better future. It ended fairly quickly but it didn't stop a smile spreading on both their faces.

John leant his forehead gently against Elizabeth's, pulling her slightly closer to his body.

'You are _never_ going offworld again' he said in a half-serious tone.

Elizabeth laughed but quickly stopped as a sharp pain sped through her body at the sudden movement.

'Hey you ok?' John asked with concern has he gently pushed her forward to examine her wounds properly.

'John. Not now. I'll be honest I haven't a clue what injuries I have but I want to get out of here _now'_

John caught the slight tone of fear that had crept into her voice. After a minute of staring at her he gave in, realising it would probably do her more harm to stay.

'Ok, but if you need to stop then tell me'

^.^.^.

'_This is team 2, we have a lock on their position. Forwarding the coordinates to you now'_

'Acknowledged…..coordinates received. Hows it going up there?'

'_A wraith hive ship and three Ongarian warships have been detected and are closing in. ETA three minutes. The Linarans have dispatched more of their ships to assist us'_

'Good, keep us updated. McKay out'

Rodney turned towards the pilot.

'OK, I've boosted the transporters as much as I can. We still need to get pretty close but beam them up as soon as possible. I've set it to automatically beam the Linaran soldiers down at the same time.'

The major replied a quick 'yes sir' before descending through the planet's atmosphere.

'Teyla, how are you doing down there?'

'_They seem to be unaware of our ships for now but they are definitely suspicious of something. We have been waiting outside the council room for almost an hour and they are still debating whether to let us in or not.'_

'What about the c4?'

'_We have planted them around the chamber. A few Linarans also transported down to our location but I am unsure of where they are hiding.'_

'Good work. Go back to the transport coordinates; Major Lorne has detected Ongarian ships and a wraith hive incoming.'

'_Understood'_

'Sir, we are about to breach the atmospheric sensors. I have contacted Major Lorne…I still cannot detect any lifesigns in the complex though sir.'

Rodney sighed and turned towards Beckett who had an equally worried look on his face.

'Keep searching Major. We might be too far away at the moment.'

Carson sighed and walked towards Rodney.

'Even if we do manage to get them aboard, I have no idea what state they'll be in. I might not be able to save them Rodney.'

Rodney stared at Carson, realising for the first time his friends fear. Unsure of what to say or do he replied with a weak smile before returning to his seat next to the pilot.

Carson turned to re-take his seat but was stopped by Ronon .

'Sheppard's alive. And if he is then so is Weir. You were made Atlantis' CMO for a reason Beckett, it'll work out.'

Carson smiled slightly as he sat down.

'Aye, I hope your right.'

^.^.^.

'Shhh its ok, I've got you'

This was the third time John had uttered those words to Elizabeth as he held her hair back whilst she was sick on the floor.

She whimpered as the gagging ceased and her body began to loosen slightly. John continued to hold her as she calmed her breathing, noticing that her vomit, again, contained blood.

'We should stop. You've got some internal injuries and I need to have a rough idea of what they are before we go on.'

'John, I've been like this for ages its nothing.' He was about to argue but was cut off by the sound of an alarm.

'Shit…' he muttered under his breath. 'C'mon, we need to move quickly.'

Elizabeth yelped as he lifted her gently into his arms. She wanted to protest but knew that this way would be a lot quicker than if she walked herself.

'Lizabeth, do you have any idea where we are?'

He stopped for a minute and observed the thoughtful look that crossed her face, only to be replaced by one of shock and fear soon after.

'Lizabeth?'

'Torture. These are the punishment chambers….they took me here and…torture' she whispered almost to herself.

Anger flooded John as he felt her grip tighten on his arm, though it was quickly replaced with concern when he saw her close her eyes, obviously trying to rid her mind of horrifying images that had suddenly come forth. He eventually felt her breathing begin to slow its pace and her grip loosened so it was no longer painfully digging into his skin.

'Keep going until you get to a red door on your right. Go through it and it leads you to the working grounds. From there we can take one of five exits which all lead to the ports.'

John tilted his head in shock at the suddenness and accuracy of her information. Elizabeth smirked slightly up at him.

'I decided to get some intel on the place's layout. I figured you'd need it when you came to save me'

He smiled and leaned down to give her a quick kiss.

'You were right' he said before starting off on a brisk walk.

^.^.^.

'Doctor McKay I'm detecting 6 lifesigns in the complex; two of them are separated from the others'

McKay looked up from his data pad at the pilot who had just spoken. He placed his hand on the controls and conjured up the map of the complex, making note of Beckett and Ronon as they moved behind him to get a better look.

'That's them, it has to be' said Carson with more hope than certainty in his voice.

'It's them' said Ronon before he went towards the back of the puddle jumper, drawing his gun to set it on kill.

'Major, get us in as close as we need as quickly as you can, one of those lifesigns is extremely weak. Beckett, go and tell the Linarans to prepare for transport then do what you and your medical team need to do in preparation. I'll let Major Lorne know what's going on.'

_Just hang in there a bit more Sheppard _he thought as he turned to contact Lorne.

^.^.^.

'Shit that was close' exclaimed Sheppard as he dropped to the floor next to Weir. They, or rather he, had just run half a mile to try and escape the Ongarian guards following them.

'We're at the working ground Liz, now where?' he turned to face the now worryingly pale face of Elizabeth Weir. She had grown quieter throughout the journey and the frantic run had managed to tire her out even more.

'Hey, baby can you hear me?'

John lifted her face so she was looking at him.

'Shit' he muttered as he observed her frighteningly blank eyes.

'Hey, lizabeth listen to me. You need to stay awake for me ok? Lizabeth!'

He shook her slightly to which she jolted awake.

'..J- John? Where…we?'

John ignored how weak her voice was and focused on answering her question.

'Hey, we're at the working grounds. I need you to stay with me ok? We're almost out of here just please stay with me'

She moaned slightly and creased her forehead in concentration.

'Nearest exit… next to the gate.' She eventually said.

John wasted no time in lifting her into his arms and running in search of the gate.

^.^.^.

'Doctor Beckett sir, one of the lifesigns is extremely weak. It's becoming very faint on the sensors. I'm going as fast as I can; we should be within range in about five minutes'

'Aye lad, thank you.'

Beckett glanced over at McKay who was trying his best to shoot him a look of encouragement. He then looked over to his awaiting medical team.

'We are ready sir. For anything that can be thrown at us' said one of the nurses with a determined smile.

Beckett smiled back, glad to see he had such a confident team.

'Aye lass. That we are.'

^.^.^.

'Finally! Liz we made it to the surface. Come on just stay with me a bit longer ok?'

'John, I can't. Pain…so tired….sleep. Love…you'

'Don't you dare Elizabeth, don't you DARE! I just found you and I will NOT lose you again ok? Just keep fighting…fight for us'

Elizabeth's eyes fluttered open as she smiled up at him.

'I love you John. If I die then know I die happy.'

'NO! Elizabeth you are NOT going to die OK?'

He placed her down gently on the ground, repeating her name over and over as he tried hard to find some remnants of a pulse.

^.^.^.

'Crap!'

'Major what's wrong?' asked McKay as he got up to stand behind the pilot.

'Sir, one of the lifesigns is gone'

'Crap! How long till we can transport?'

'One minute sir'

McKay lightly clapped the pilots shoulder then turned towards Beckett who, judging by the look on his face, had heard the update.

Beckett nodded to McKay and turned to the rest of the jumper's occupants.

'We're a minute away from transport. Everyone get ready. Medical team…we have a problem…'

**Mwahahahaha cliffhanger! Sorry, I'm mean but hey, this was a good place to stop. As said, I will try and update ASAP. Reviews make me happy! :D**


	11. Chapter 11

**Well this is a short one that I felt like doing...it leads nicely into my final chapter which will be the next one! I am sad that this is almost coming to an end but thanks to all who have stayed with this from the beginning.**

'Sir we're within range but I still can't get the other life sign back.'

McKay stood up to get a better view of the screen.

'Ok people change of plan! We are going to land the jumper as close to them as we can, got it Major?'

'Yes sir'

'Right, the map shows the Ongarians are closing in on their position. Ronon, ideas?'

'Two stay and take point at the jumper. Me and the rest will go and get Sheppard and Weir'

McKay nodded his approval and pulled Beckett out of the way as the soldiers prepared to disembark.

'Carson…just do your best.' He said, swiftly followed by an awkward yet friendly pat on the back.

'Beginning descent, everyone hang on. Touch down in 3, 2, 1…'

The floor of the jumper shuddered slightly as it landed. McKay moved to the console to release the jumper hatch.

'Let's move!' shouted Ronon as he and the Linaran soldiers moved out.

Ronon moved as cautiously and quickly as he could, grateful that the Linaran soldiers were able to keep up. They followed McKay's instructions over the radio until they came across some Ongarian soldiers.

Making quick work of taking them out, they continued following McKay's instructions until a cry of utter desperation filled the air.

'LIZABETH! DAMMIT LIZ WAKE UP!'

Ronon sprinted towards his commanding officer, not even bothering to follow McKay's frantic instructions. He was glad to hear the Linarans sprinting after him, ready to assist if need be.

He finally turned a corner and froze at the sight. Sheppard had blood down his face and he looked frighteningly thin. But the worst part was the still and deathly pale form of Elizabeth Weir on the ground. Without a word, Ronon lifted Elizabeth into his arms and sprinted off towards the jumper, leaving an angry and bewildered Sheppard to the care of the Linarans.

'Beckett! I have Weir and she isn't breathing. The Linarans are gonna bring in Sheppard, he doesn't look so good either.'

'Understood' was Beckett's reply before Ronon heard him issuing numerous orders to his medical team.

Ronon reached the jumper in record time and carefully placed Elizabeth on a makeshift bed on the jumper floor.

'Oh dear Lord' he heard Beckett mutter before he once again left to go back for Sheppard.

He met him half way, trying to fight off the Linarans but without much success. He ceased fighting, however, when he caught sight of Ronon.

'Ronon! Where is Elizabeth. Where is she?' Ronon caught him as he tried to rush past him.

'Sheppard! Cool it. Beckett and his team have her, she _will_ be ok Sheppard' he said with as much conviction as he could. He held John firmly in place until he was sure his friend would stop hyperventilating.

'Take…Take me to her…please' he added quietly after a while. The events of the past few hours were beginning to take its toll and Sheppard could barely remain standing. Sensing this, Ronon offered to act as a support for Sheppard, which he gladly took, and together they headed off to the jumper.

As they approached, Ronon nodded to the two Linaran guards to dismiss them to help their comrades in the complex. They did a brief salute then ran off in the opposite direction.

'So…allies?' asked Sheppard weakly.

'Linarans. Pretty useful warriors. Hate the Ongarians. Used to be one race and all that' was Ronon's short reply.

It took a few more steps for them to finally reach the jumper where Ronon, again, had to keep hold of John to prevent him getting in the way of Carson and his team.

'Again!' shouted Carson, paying no attention to the two men in the doorway.

The sound of the defibrillator echoed in the otherwise silent jumper. Everyone was looking hopefully as Beckett tried his best to revive their leader.

'Still no pulse.' replied a nurse

'No….no no no no no! ELIZABETH!' John fought as much as he could to try and get out of Ronon's grip but the Satedan warrior was far too strong.

'Sir, make sure he stays still. He could be doing himself more harm' advised another nurse to Ronon, indicating the jumper bench.

Ronon lifted John up and placed him on one of the jumper's benches, making sure to keep him pinned down, to avoid him moving. John was screaming Elizabeth's name as he tried to fight the oncoming darkness.

'Goddammit Elizabeth come back to us…' John heard Carson say.

He fell quiet as all his energy suddenly slipped from him. A tear rolled down his cheek as he heard the sound of the flat-lined bleep that echoed throughout the silent jumper.

'Carson?' was the last thing John heard before he succumed to darkness.

**Again mean I know :P And I know it's a short chapter but next one will be the finale and longer so look out for that. Reviews as usual! :D**


	12. Chapter 12

**It's the final chapter! I can't belive I actually updated it this soon! :) Would like to know how you found it so REVIEWS! I'm considering writing another fic (damn plot bunny decided to pay a visit :P), it probably won't be as dark but it will be Sparky! For now though, enjoy!**

'Colonel Sheppard…John…'

John tried to focus on the voice as it called to him. He recognised the voice. It took him longer than it should have to place the Scottish accent of Carson Beckett but he got there eventually.

'Carson?' he croaked, voice sounding hoarse from lack of use.

'Hello son, gave us a fright there. How you feelin?' came the cheery reply.

'Carson…' John opened his eyes and blinked to adjust them to the light. 'What…happened?' he asked, his memory still painfully cloudy.

'You were extremely malnourished and had a broken nose. There was some device in your head as well but we were able to remove it without any damage…that'd be why your memory is foggy.' He replied with a slight smile.

John, now able to fully open his eyes, stared at the welcoming face of his friend. For the first time in what felt like ages he smiled.

'S' good to…see you Carson…' he reached his hand slowly upward and gripped the doctor's arm. 'How long?' he asked, slightly dreading the answer.

'I had to induce a coma; you've been out of it for a week son. You woke up earlier than I expected'

'Reason why…' John muttered as the familiar darkness once again tried to claim it.

'Don't fight it son, go back to sleep.' Carson patted the Colonel's shoulder and made to move away but was stopped by a firm grip on his arm.

'Lizabeth! Carson, is she…is she…' he broke off as a tear threatened to escape down his face.

Carson stared at John for a moment, holding his gaze, an internal battle waging in his head.

'Dammit Carson TELL ME! EVERYTHING, I NEED TO KNOW!' shouted John with more force than he should have been capable of.

Carson sighed and turned to look at Rodney who had just entered the infirmary. After receiving a slight nod from the scientist, Carson grabbed a chair and pulled it next to John's bed.

'…Elizabeth is alive Colonel. We managed to save her, thanks to the Linaran's help but it was a damn close one. We lost her a few more times during and after surgery,' he smiled slightly as he saw the tears well up in the military commander's face.

'Can I see her?' he asked after a while

Carson shook his head. 'No son you can't. We've put her in isolation to help her recovery. She was severely injured and it will take a long while for her to fully recover...' Carson paused to look up again at Rodney who was now standing at the foot of John's bed.

'What aren't you telling me Carson?' asked John, trying harder than ever to fight for control to stay awake.

Carson sighed, knowing that the Colonel really shouldn't be hearing about this in his current state.

'She's in a coma and I can't bring her out of it. There is a good chance she won't come out of it and even if she does…they'll be no guarantee that she'll be the same Elizabeth Weir we know. From her injuries, I have a pretty good idea what she went through. The human body isn't designed to withstand so much trauma and Elizabeth was not trained to deal with anything like this. Her mind could just collapse in on itself…'

Carson sympathetically patted John's shoulder as he saw the Colonel struggle to hold back the tears. After a moment of regaining his composure, John looked up at Carson.

'There is still…a chance she will…make...it?'

'Aye, but at the moment it is worryingly small.'

John stared at Carson, satisfied that he had been told everything. He closed his eyes, finally giving into the need to sleep.

'There is still a chance… that's enough for…me'

Carson merely smiled as his patient finally fell asleep.

*.*.*.*.*

**3 months later…**

'Finally!' exclaimed an excited Rodney as he entered Elizabeth's office to find a puzzled John and Teyla.

'The Ongarians have finally fallen. The Linarans have seized all their territory and want to open official negotiations when they've sorted themselves out.'

'This is good news' smiled Teyla encouragingly at John who continued to stare at an ornament on Elizabeth's desk.

'And!' continued Rodney, oblivious to John's more-than-usual solemn mood. 'Any alliance we have with the Linarans will effectively get the IOA off our backs for the whole disobeying orders thing' He smiled proudly but stopped when he noticed John, still staring at the ornament.

'Sheppard?' he eventually asked, ignoring the cautioning look from Teyla.

'I'm going for a run' he replied after a while. He got up and left the room without a backward glance.

*.*.*.*.*

'John? John!'

John stopped jogging and turned to face Teyla as she ran towards him.

'Hey, what's up?'

'We have been trying to contact you for about an hour. Where is your headset?' she queried, concern etching her face as she studied her friend. Whilst John had made a full recovery, he still had to put up with insomnia from his nightmares, not to mention the fact that he was worried sick about Elizabeth. He always looked tired and was no longer the cheeky military commander they once knew.

'I urm, left it?' he replied weakly, realising Teyla was one of the people he could not lie to.

Sighing, she decided to just get to the point.

'Carson wants you in the infirmary now…Elizabeth has- John!'

John sprinted as soon as Elizabeth was mentioned.

_God Lizabeth please be ok please please please be ok_ he thought as he made no attempt to avoid people in the hallways.

He had been trying to prepare for this moment for three months yet he suddenly realised that nothing he did, or could have done, would ever prepare him for this.

'Carson!' he shouted as soon as he ran into the infirmary. She had been moved there about two weeks ago when Carson finally deemed all her physical injuries healed.

'Colonel! I've been tryin to contact you for ages. Where've you been?' he asked, but John ignored him as he heard a soft voice behind the closed curtains.

'John?'

John's heart raced and he wasted no time in slipping through the gap in the curtains. His smile grew ten-fold as his eyes met the equally green and tired ones of Elizabeth Weir.

'You're awake' he whispered, afraid if he said it louder then it would, somehow, not be true.

'John.' She said with more strength in her voice this time.

He smiled, as did she, and moved over to envelope her in a hug. He held her as tightly as he dared, noting that her body was still thin and felt just as fragile as it had the last time he held her.

'God I missed you so much' he whispered into her hair, kissing the top of her head as he felt her hot tears soak through his shirt.

She continued to cry and John felt her begin to shake. He pulled away and wiped her tears from her face, then lifted her chin so her gaze met his. He smiled slightly when she stopped crying.

'Hey.' He whispered as he caressed her cheek.

'Hey…' she whispered back before leaning her forehead against his.

'Colonel, sorry to interrupt but I was tryin to say that I need to run some tests' interrupted Carson as he came through the curtains with a tray full of equipment in tow.

John glanced over at the various tools and got the message. Releasing Elizabeth's face he went to move away.

'John! No stay, please stay.' She almost cried to both men's shock.

John looked at Carson imploringly to which he sighed and turned to Elizabeth.

'Lass, I have no problem with the colonel stayin, but, the tests I need to do are somewhat…private' he winced as he saw the colour drain completely from her face.

After a while she moved to grasp John's hand and muttered a quiet 'stay'

John looked over to Carson to which he received a nod. He then positioned himself on the edge of the bed by her side, facing away from her lower half to give her some privacy and gripped her hands in his, offering as much support as he could.

She whimpered when Carson went to move her blankets away from her lower body and started screaming as he made to remove her clothing.

'Lizabeth baby it's me, John remember. You're safe now, you're in Atlantis. Carson is here too and he won't hurt you…no one will hurt you ever again.' She started to calm at his words but she was still moving away from Carson's touch.

'I love you Liz. Trust me. Please. You're not back there you're here with us…with me.' he begged, bending down to lean his head against hers. She finally settled, crying silently and gripping onto John as if her life depended on it.

'Good, now Elizabeth, I need to take a look at you ok? You were wounded very badly and I need to make sure it's all ok so can you trust me?' asked Carson, afraid of traumatising his patient further.

'Trust…' she whispered, followed by an even quieter 'Yes.' She tightened her grip further on John.

'Ok, now I'm just going to remove your trousers ok. You don't need to worry about anything ok?'

Elizabeth whimpered as Carson removed her trousers and underwear. She pulled John closer to her when she felt Carson move closer.

'S'ok Elizabeth. I'm here ok? I'm always gonna be here now'

He continued offering her words of comfort until Carson finally finished with his examination. He then moved to make adjustments to her IV bag.

'OK colonel, she needs to have a rest now. I've given you something to help you sleep lass. Colonel, I'll be outside when you're ready.'

John watched as Carson walked through the curtains then turned back to see Elizabeth fighting off sleep.

'Hey, don't fight it. The more you rest the quicker you beat this thing ok?'

He kissed her cheek and tried to leave but was stopped by her iron grip on his hand.

'John. Don't leave me please. The nightmares… Just stay with me' she begged, close to tears again.

John smiled what he hoped to be a reassuring smile.

'Let me go and see Carson quickly then I promise you I'll be back'

He watched as she mulled over his proposition and smiled when she eventually gave a faint nod and released his hand. He leaned down again to kiss her forehead then walked out to a waiting Carson.

'Colonel, her wounds have healed but they will bring some…problems…to her future. They are rather personal but seeing the change in your relationship…you are probably entitled to know?' he asked, trying to gage the Colonel's response.

After a while, John gave a stiff nod.

Sighing, Carson moved to his computer and brought up some recent scans of Elizabeth. Once John had followed him, he began indicating certain areas on the diagram whilst explaining the damage. It was a good half hour before they were done and John gave a tired and forced smile to the Doctor before he made his way back to Elizabeth's bed.

'Hey.' He smiled at her, surprised to see her still awake.

She just stared at him as he moved towards her and it was then that he realised she'd been crying.

'Nightmares?' he asked as he pulled her gently towards him in a hug. She merely nodded slightly against his chest. He could feel her trying to even out her breathing.

After a while she pushed away slightly to look at him.

'I overheard. Carson said there was something wrong. Tell me?' she asked, her eyes pleading with him.

John stared at her for a moment as he considered his next words carefully.

'Elizabeth…remember that I love you no matter what. This wasn't your fault, none of it was ok? Just remember that?' he waited for her to nod before speaking again.

'You can't have children. There was too much damage done to your…lower anatomy…Doc reckons with the knife?' he trailed off as he observed her face change at the memories of what had happened. He pulled her closer towards him as she began to cry.

'God John, I'm sorry I'm-'

'No. Liz. Not your fault remember?' he pressed, pulling her face up to meet his, making sure he got the message through to her.

She nodded slightly before moving back to bury her head in John's chest.

He held her while she cried, not just about the latest news but from the whole ordeal. John was glad she didn't keep it all in. To him, this was one huge step in the right direction.

He turned his head slightly when a movement caught his eye; Carson was standing there with Teyla, Ronon and McKay. The men stood there, Ronon and Rodney looking slightly uncomfortable. They gave a slight nod towards John before departing. Teyla, however, moved slowly towards Elizabeth and reached down to give her a light kiss on the head.

John noticed her tense slightly but was relieved when she relaxed and uttered a quiet 'thank you Teyla' before re-burying her face into John's chest. Teyla then gave John a friendly rub on the back before smiling at Carson and also leaving.

Carson stood there and stared at the couple for a minute. He was glad to see Elizabeth was at least opening up to someone but he was still concerned about a few of her injuries. As for when he could release her to active duty, he had no idea. He wasn't even sure if she would ever be fit for leading Atlantis again.

The latter thought was quickly banished though when he noticed Elizabeth lift her head to give John a light kiss at something that he'd said.

He smiled to himself before turning away, comforted by the thought that she had John and the rest of Atlantis to help her recover.

_We will get you back lass_ he thought. _John won't let us stop until we do_.

*.*.*.*.*

**2 years later…**

'Come on, just push once more then it's all over' prompted the Doctor. The woman screamed as she pushed with all her strength. The brief minute felt like an eternity as the pain coursed through her body. But then suddenly, it stopped. And she knew from the cries filling the room that the baby was born.

'It's a girl' said the Doctor. He gave her to the nurse who took her to the side of the room to get cleaned up. The woman gave a tired laugh as she looked over at the couple standing by her.

'You have a baby girl' she said to them, watching as tears filled their eyes. She smiled as she observed the shocked and happy couple; the man was watching the baby as the nurses gently wrapped her in a blanket. The woman, who was holding her hand, was staring at her in disbelief.

'Thank you…' the standing woman said softly, then squeezed the hand she was holding. 'Thank you so much for giving us this baby' she said on the verge of tears. Her husband had heard her tone of voice and came over to envelope her in a hug.

'Here is your daughter' said the nurse, staring at the birth mother for a minute and then the woman standing, unsure of who to give the baby to.

'She belongs to them' smiled the birth mother, noticing the nurse's dilemma.

The nurse nodded and handed the baby to the woman standing, smiling as she saw the man move closer to her to get a better look of their baby.

'Lizabeth…we have a baby girl' he spoke after a while, a ridiculously large grin spreading across his face.

Elizabeth looked behind her at her husband. She just stared at him, memories of their times together all flashing through her mind. From their first kiss on the Ongarian home-world, to their marriage and now to this; the moment they had long waited for.

'Lizabeth? You ok?' asked John with concern as her face went suddenly thoughtful. He placed his hand on her lower back slightly, trying to gain a reaction from her.

'No.' she replied after a while, smiling as his face turned immediately worried.

'We have a baby John, I'm so much better than ok' she laughed as she looked down at the sleeping bundle in her arms.

John smiled and leant down to lightly kiss the baby's head. He then turned to the woman on the bed who was staring up at them with a grin plastered on her face.

'Thank you so much' he said as he moved to lean down and kiss the woman on the forehead.

'I'm glad I chose you two' she said smiling up at them.

'Ok, we need to move you to the other room now' said a nearby nurse.

'Thank you so much…I can never express fully how much this means to us' said Elizabeth as she reached down to show the baby to the other woman.

The woman smiled and stroked the baby's head. 'I know you'll take good care of her. I wish I could live to see her grow up' she added sadly.

Elizabeth gave her a sad smile. 'We will tell her about you…about how wonderful and kind you have been' she said as she hugged the other woman. The woman nodded against Elizabeth's shoulder, tears now slipping slowly down her face.

'Please, tell her why I couldn't be there for her' she begged, hugging Elizabeth closer when she felt the woman nod fiercely.

'Of course we will' Elizabeth reassured as she separated from the woman and took the baby carefully in her arms.

'Ma'am, we need to move you now.' Stated the Doctor this time. The woman nodded at him before turning back to Elizabeth and John.

'What will you call her?' asked the woman

Elizabeth smiled up at John who smiled back.

'We were thinking, Rachel Sheppard, after you' smiled John as he saw tears once again well up in the woman's eyes.

'Thank you' replied Rachel quietly before she leaned back against the pillow and closed her eyes. Elizabeth smiled and leant against John as he brought his arms around her and the baby.

'I die happy.' were the last words Elizabeth and John heard from the woman before she was wheeled out of the room.

*.*.*.*.*

'Chevron seven locked'

John looked up as the wormhole opened. They had been on Earth for three weeks now and were eager to take the newest member of their family back to Atlantis.

'Doctor Weir, Colonel Sheppard…little Sheppard' came the voice of Jack O'Neill as he came down the ramp from the wormhole. 'Atlantis is eager to have you back. Preparations for your new addition have all been made' he said, smiling down as Rachel grabbed his finger in her tiny hand.

'I still can't believe the IOA are ok with this' muttered John as Elizabeth handed Jack the baby.

'They didn't have much of a choice John. Atlantis is a colony and has been for a while…the IOA don't rule us anymore.' She said, not bothering to hide the pride in her voice.

'Indeed they don't. Now, you two better get going. And you little lady, stay safe' he added as he passed the baby over to John's waiting arms.

'Thank you Jack, for everything' said Elizabeth as she moved to hug Jack.

'Yes sir…thank you' nodded John politely.

'Any time' he smiled before moving out of their way.

John turned to Elizabeth as she grabbed his hand.

'Here we go' he said. 'I told you this day would come' he smiled before leaning down to steal a quick kiss.

'Yes you did' she replied. 'Thank you' she added.

'For what?'

'For helping me recover. And for staying with me all this time. ' she replied before squeezing his hand.

John smiled and pulled her closer to him.

'Come on, let's get this little one home.'

**The end :D – of course I didn't kill Elizabeth! Hope you all enjoyed, thank you all again for reading, rating and reviewing; has been encouraging to have your constant support, even when I didn't update for ages :P**


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